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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 40, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Modified from penetest.py file in CHARMM-GUI" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import argparse\n", | |
| "import sys\n", | |
| "import networkx as nx\n", | |
| "import re\n", | |
| "import numpy as np\n", | |
| "import itertools" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import MDAnalysis as mda" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "_s = re.compile('\\s+')\n", | |
| "_p = re.compile('(\\d+)\\s+(\\d+)')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def lsqp(atoms):\n", | |
| " com = atoms.mean(axis=0)\n", | |
| " #u, d, v = np.linalg.svd(atoms-com)\n", | |
| "\n", | |
| " axes = np.zeros((len(atoms), 3))\n", | |
| " for i in range(len(atoms)):\n", | |
| " p1 = atoms[i]\n", | |
| " if i == len(atoms)-1:\n", | |
| " p2 = atoms[0]\n", | |
| " else:\n", | |
| " p2 = atoms[i+1]\n", | |
| " a = np.cross(p1, p2)\n", | |
| " axes += a\n", | |
| " u, d, v = np.linalg.svd(axes)\n", | |
| " i = 0\n", | |
| " d = -np.dot(v[i], com)\n", | |
| " n = -np.array((v[i,0], v[i,1], d))/v[i,2]\n", | |
| " return v[i], com, n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def intriangle(triangle, axis, u, p):\n", | |
| " # http://www.softsurfer.com/Archive/algorithm_0105/algorithm_0105.htm\n", | |
| " p1, p2, p3 = triangle\n", | |
| " w0 = p - p1\n", | |
| " a = -np.dot(axis, w0)\n", | |
| " b = np.dot(axis, u)\n", | |
| " if (abs(b) < 0.01): return False\n", | |
| "\n", | |
| " r = a / b\n", | |
| " if r < 0.0: return False\n", | |
| " if r > 1.0: return False\n", | |
| "\n", | |
| " I = p + u * r\n", | |
| "\n", | |
| " u = p2 - p1\n", | |
| " v = p3 - p1\n", | |
| " uu = np.dot(u, u)\n", | |
| " uv = np.dot(u, v)\n", | |
| " vv = np.dot(v, v)\n", | |
| " w = I - p1\n", | |
| " wu = np.dot(w, u)\n", | |
| " wv = np.dot(w, v)\n", | |
| " D = uv * uv - uu * vv\n", | |
| "\n", | |
| " s = (uv * wv - vv * wu)/D\n", | |
| " if (s < 0 or s > 1): return False\n", | |
| " t = (uv * wu - uu * wv)/D\n", | |
| " if (t < 0 or (s+t) > 1): return False\n", | |
| " return True" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def build_topology(universe, selection):\n", | |
| " g = nx.Graph()\n", | |
| "\n", | |
| " # Atoms\n", | |
| " natom = universe.atoms.n_atoms\n", | |
| " for atom in universe.select_atoms(selection).atoms: # might be buggy\n", | |
| " g.add_node(atom.index + 1, **{'segid': atom.segid,\n", | |
| " 'resname': atom.resname,\n", | |
| " 'name': atom.name,\n", | |
| " 'resid': atom.resid})\n", | |
| " # Bonds\n", | |
| " for bond in universe.select_atoms(selection).bonds:\n", | |
| " num1, num2 = bond.atoms.indices + 1\n", | |
| " if g.has_node(num1) and g.has_node(num2):\n", | |
| " g.add_edge(num1, num2)\n", | |
| " return g" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 28, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def check_ring_penetration(top, coord, pbc=[], xtl='rect', verbose=0):\n", | |
| " # ring penetration test\n", | |
| " # 1. find rings\n", | |
| " # 2. build least square plane\n", | |
| " # 3. project atoms ring constituent atoms onto the plane and build convex\n", | |
| " # 4. find two bonded atoms that are at the opposite side of the plane\n", | |
| " # 5. determine the point of intersection is enclosed in the ring\n", | |
| " #\n", | |
| " from networkx.algorithms.components import connected_components\n", | |
| " molecules = (top.subgraph(c) for c in connected_components(top))\n", | |
| "\n", | |
| " allatoms = np.array([coord[num] for num in top.nodes()])\n", | |
| " atoms_map = np.array([num for num in top.nodes()])\n", | |
| " natoms = len(allatoms)\n", | |
| " if pbc:\n", | |
| " atoms_map_reverse = {}\n", | |
| " for i,num in enumerate(top.nodes()):\n", | |
| " atoms_map_reverse[num] = i\n", | |
| "\n", | |
| " a = float(pbc[0])\n", | |
| " b = float(pbc[1])\n", | |
| " n = len(allatoms)\n", | |
| " if xtl == 'rect':\n", | |
| " allatoms = np.tile(allatoms, (9,1))\n", | |
| " op = ((a,0),(a,b),(0,b),(-a,b),(-a,0),(-a,-b),(0,-b),(a,-b))\n", | |
| " for i in range(8):\n", | |
| " x,y = op[i]\n", | |
| " allatoms[n*(i+1):n*(i+2),0] += x\n", | |
| " allatoms[n*(i+1):n*(i+2),1] += y\n", | |
| " atoms_map = np.tile(atoms_map, 9)\n", | |
| " if xtl =='hexa':\n", | |
| " allatoms = np.tile(allatoms, (7,1))\n", | |
| " rot = lambda theta: np.matrix(((np.cos(np.radians(theta)), -np.sin(np.radians(theta))),\n", | |
| " (np.sin(np.radians(theta)), np.cos(np.radians(theta)))))\n", | |
| " op = (rot(15), rot(75), rot(135), rot(195), rot(255), rot(315))\n", | |
| " d = np.array((a, 0))\n", | |
| " for i in range(6):\n", | |
| " xy = np.dot(d, op[i])\n", | |
| " allatoms[n*(i+1):n*(i+2),:2] = allatoms[n*(i+1):n*(i+2),:2] + xy\n", | |
| " atoms_map = np.tile(atoms_map, 7)\n", | |
| "\n", | |
| " # print out image atoms\n", | |
| " #fp = open('image.pdb', 'w')\n", | |
| " #for i,atom in enumerate(allatoms):\n", | |
| " # x, y, z = atom\n", | |
| " # fp.write(\"HETATM%5d %-3s %3s %4d %8.3f%8.3f%8.3f 0.00 0.00 \\n\" % (i, 'C', 'DUM', i, x, y, z))\n", | |
| "\n", | |
| " pen_pairs = []\n", | |
| " pen_cycles = []\n", | |
| "\n", | |
| " for m in molecules:\n", | |
| " cycles = nx.cycle_basis(m)\n", | |
| " if not cycles: continue\n", | |
| " for cycle in cycles:\n", | |
| " flag = False\n", | |
| " atoms = np.array([coord[num] for num in cycle])\n", | |
| " if len(set([top.nodes[num]['resid'] for num in cycle])) > 1: continue\n", | |
| " if verbose:\n", | |
| " num = cycle[0]\n", | |
| " print('found ring:', top.nodes[num]['segid'], top.nodes[num]['resid'], top.nodes[num]['resname'])\n", | |
| "\n", | |
| " # build least square fit plane\n", | |
| " axis, com, n = lsqp(atoms)\n", | |
| "\n", | |
| " # project atoms to the least square fit plane\n", | |
| " for i,atom in enumerate(atoms):\n", | |
| " w = np.dot(axis, atom-com)*axis + com\n", | |
| " atoms[i] = com + (atom - w)\n", | |
| "\n", | |
| " maxd = np.max(np.sqrt(np.sum(np.square(atoms - com), axis=1)))\n", | |
| "\n", | |
| " d = np.sqrt(np.sum(np.square(allatoms-com), axis=1))\n", | |
| " nums = np.squeeze(np.argwhere(d < 3))\n", | |
| "\n", | |
| " # find two bonded atoms that are at the opposite side of the plane\n", | |
| " for num in nums:\n", | |
| " num1 = atoms_map[num]\n", | |
| "\n", | |
| " for num2 in top[num1]:\n", | |
| " if num1 in cycle or num2 in cycle: continue\n", | |
| " if num > natoms:\n", | |
| " # image atoms\n", | |
| " offset = int(num / natoms)\n", | |
| " coord1 = allatoms[num]\n", | |
| " coord2 = allatoms[atoms_map_reverse[num2] + offset * natoms]\n", | |
| " else:\n", | |
| " coord1 = coord[num1]\n", | |
| " coord2 = coord[num2]\n", | |
| "\n", | |
| " v1 = np.dot(coord1 - com, axis)\n", | |
| " v2 = np.dot(coord2 - com, axis)\n", | |
| " if v1 * v2 > 0: continue\n", | |
| "\n", | |
| " # point of intersection of the least square fit plane\n", | |
| " s = -np.dot(axis, coord1-com)/np.dot(axis, coord2-coord1)\n", | |
| " p = coord1 + s*(coord2-coord1)\n", | |
| "\n", | |
| " d = np.sqrt(np.sum(np.square(p-com)))\n", | |
| " if d > maxd: continue\n", | |
| " if verbose:\n", | |
| " print('found potentially pentrarting bond:',\n", | |
| " top.nodes[num1]['segid'],\n", | |
| " top.nodes[num1]['resid'],\n", | |
| " top.nodes[num1]['resname'],\n", | |
| " top.nodes[num1]['name'],\n", | |
| " top.nodes[num2]['name'])\n", | |
| "\n", | |
| " d = 0\n", | |
| " for i in range(0, len(atoms)):\n", | |
| " p1 = atoms[i] - p\n", | |
| " try: p2 = atoms[i+1] - p\n", | |
| " except: p2 = atoms[0] - p\n", | |
| " d += np.arccos(np.dot(p1, p2)/np.linalg.norm(p1)/np.linalg.norm(p2))\n", | |
| "\n", | |
| " wn = d/2/np.pi\n", | |
| " if wn > 0.9 and wn < 1.1:\n", | |
| " # we have a case\n", | |
| " pen_pairs.append((num1, num2))\n", | |
| " pen_cycles.append(cycle)\n", | |
| " flag = True\n", | |
| " break\n", | |
| "\n", | |
| " if flag: break\n", | |
| "\n", | |
| " return pen_pairs, pen_cycles" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 31, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "def check_universe_ring_penetration(universe):\n", | |
| " selection = 'not resname TIP3 and not (name H*)'\n", | |
| " \n", | |
| " top = build_topology(universe, selection)\n", | |
| " ag = universe.select_atoms(selection)\n", | |
| " for frame, ts in enumerate(universe.trajectory):\n", | |
| " print('In frame', frame)\n", | |
| " coord = dict(zip(ag.ids + 1, ag.positions))\n", | |
| " if len(top.nodes()) != len(coord):\n", | |
| " raise AtomMismatch('Number of atoms does not match')\n", | |
| "\n", | |
| " print('%lipid ring pentration')\n", | |
| " \n", | |
| " # only rect pbc have been tested\n", | |
| " pairs, rings = check_ring_penetration(top, coord)\n", | |
| " if pairs:\n", | |
| " print('found a ring penetration:')\n", | |
| " for i, cycle in enumerate(rings):\n", | |
| " print('- %s %s %s %s | %s %s %s %s' % (top.nodes[pairs[i][0]]['segid'], top.nodes[pairs[i][0]]['resid'], top.nodes[pairs[i][0]]['resname'], ' '.join([top.nodes[num]['name'] for num in pairs[i]]), top.nodes[cycle[0]]['segid'], top.nodes[cycle[0]]['resid'], top.nodes[cycle[0]]['resname'], ' '.join([top.nodes[num]['name'] for num in cycle])))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 33, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n", | |
| "found a ring penetration:\n", | |
| "- seg_7_SAPI24 2779 SAPI24 C36 C37 | seg_0_PROA 946 TRP CE2 CZ2 CH2 CZ3 CE3 CD2\n", | |
| "- seg_5_PLPE 2398 PLPE C23 C24 | seg_0_PROA 1266 TRP CD1 NE1 CE2 CD2 CG\n", | |
| "- seg_3_PLPI 2123 PLPI C34 C35 | seg_0_PROA 1264 PRO CD CG CB CA N\n", | |
| "- seg_7_SAPI24 2772 SAPI24 C38 C39 | seg_1_PROB 1665 PHE CD1 CE1 CZ CE2 CD2 CG\n", | |
| "- seg_4_POPC 2261 POPC C23 C24 | seg_2_CHL1 1947 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_3_PLPI 2125 PLPI C310 C311 | seg_2_CHL1 1956 CHL1 C14 C13 C12 C11 C9 C8\n", | |
| "- seg_5_PLPE 2454 PLPE C34 C35 | seg_2_CHL1 1970 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2331 POPC C213 C214 | seg_2_CHL1 1978 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_4_POPC 2372 POPC C36 C37 | seg_2_CHL1 1982 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2623 PLPC C215 C216 | seg_2_CHL1 1983 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2881 PLPA C310 C311 | seg_2_CHL1 1992 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2879 PLPA C212 C213 | seg_2_CHL1 1997 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2604 PLPC C212 C213 | seg_2_CHL1 1998 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2166 PLPI C311 C312 | seg_2_CHL1 2001 CHL1 C6 C7 C8 C9 C10 C5\n", | |
| "- seg_6_PLPC 2523 PLPC C26 C27 | seg_2_CHL1 2009 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_6_PLPC 2523 PLPC C215 C216 | seg_2_CHL1 2009 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2601 PLPC C28 C29 | seg_2_CHL1 2014 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_8_POPA 2825 POPA C25 C26 | seg_2_CHL1 2017 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_9_PLPA 2869 PLPA C26 C27 | seg_2_CHL1 2019 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2589 PLPC C310 C311 | seg_2_CHL1 2027 CHL1 C14 C15 C16 C17 C13\n", | |
| "- seg_6_PLPC 2564 PLPC C315 C316 | seg_2_CHL1 2027 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2532 PLPC C216 C217 | seg_2_CHL1 2028 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_5_PLPE 2404 PLPE C313 C314 | seg_2_CHL1 2036 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2270 POPC O21 C21 | seg_2_CHL1 2041 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_3_PLPI 2186 PLPI C315 C316 | seg_2_CHL1 2042 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_9_PLPA 2861 PLPA C25 C26 | seg_2_CHL1 2048 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_6_PLPC 2598 PLPC C210 C211 | seg_2_CHL1 2062 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2123 PLPI C215 C216 | seg_2_CHL1 2066 CHL1 C16 C15 C14 C13 C17\n", | |
| "- seg_6_PLPC 2564 PLPC C213 C214 | seg_2_CHL1 2069 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_4_POPC 2334 POPC C35 C36 | seg_2_CHL1 2070 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_4_POPC 2334 POPC C39 C310 | seg_2_CHL1 2070 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2637 PLPC C39 C310 | seg_2_CHL1 2084 CHL1 C6 C5 C10 C9 C8 C7\n", | |
| "- seg_6_PLPC 2569 PLPC C36 C37 | seg_2_CHL1 2089 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_6_PLPC 2541 PLPC C211 C212 | seg_2_CHL1 2112 CHL1 C5 C6 C7 C8 C9 C10\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/em.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/em.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 39, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n", | |
| "found a ring penetration:\n", | |
| "- seg_7_SAPI24 2772 SAPI24 C38 C39 | seg_1_PROB 1665 PHE CD1 CE1 CZ CE2 CD2 CG\n", | |
| "- seg_4_POPC 2261 POPC C23 C24 | seg_2_CHL1 1947 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_3_PLPI 2125 PLPI C310 C311 | seg_2_CHL1 1956 CHL1 C14 C13 C12 C11 C9 C8\n", | |
| "- seg_5_PLPE 2454 PLPE C34 C35 | seg_2_CHL1 1970 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2331 POPC C213 C214 | seg_2_CHL1 1978 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_4_POPC 2372 POPC C36 C37 | seg_2_CHL1 1982 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2623 PLPC C215 C216 | seg_2_CHL1 1983 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2881 PLPA C310 C311 | seg_2_CHL1 1992 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2879 PLPA C212 C213 | seg_2_CHL1 1997 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2604 PLPC C212 C213 | seg_2_CHL1 1998 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2166 PLPI C311 C312 | seg_2_CHL1 2001 CHL1 C6 C7 C8 C9 C10 C5\n", | |
| "- seg_6_PLPC 2523 PLPC C26 C27 | seg_2_CHL1 2009 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_6_PLPC 2523 PLPC C215 C216 | seg_2_CHL1 2009 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2601 PLPC C28 C29 | seg_2_CHL1 2014 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_8_POPA 2825 POPA C25 C26 | seg_2_CHL1 2017 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_9_PLPA 2869 PLPA C26 C27 | seg_2_CHL1 2019 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2589 PLPC C310 C311 | seg_2_CHL1 2027 CHL1 C14 C15 C16 C17 C13\n", | |
| "- seg_6_PLPC 2564 PLPC C315 C316 | seg_2_CHL1 2027 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2532 PLPC C216 C217 | seg_2_CHL1 2028 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_5_PLPE 2404 PLPE C313 C314 | seg_2_CHL1 2036 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2270 POPC O21 C21 | seg_2_CHL1 2041 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_3_PLPI 2186 PLPI C315 C316 | seg_2_CHL1 2042 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_9_PLPA 2861 PLPA C25 C26 | seg_2_CHL1 2048 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_6_PLPC 2598 PLPC C210 C211 | seg_2_CHL1 2062 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2123 PLPI C215 C216 | seg_2_CHL1 2066 CHL1 C16 C15 C14 C13 C17\n", | |
| "- seg_6_PLPC 2564 PLPC C213 C214 | seg_2_CHL1 2069 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_4_POPC 2334 POPC C35 C36 | seg_2_CHL1 2070 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_4_POPC 2334 POPC C39 C310 | seg_2_CHL1 2070 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2637 PLPC C39 C310 | seg_2_CHL1 2084 CHL1 C6 C5 C10 C9 C8 C7\n", | |
| "- seg_6_PLPC 2569 PLPC C36 C37 | seg_2_CHL1 2089 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_6_PLPC 2541 PLPC C211 C212 | seg_2_CHL1 2112 CHL1 C5 C6 C7 C8 C9 C10\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 35, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n", | |
| "found a ring penetration:\n", | |
| "- seg_4_POPC 2261 POPC C23 C24 | seg_2_CHL1 1947 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_3_PLPI 2125 PLPI C310 C311 | seg_2_CHL1 1956 CHL1 C14 C13 C12 C11 C9 C8\n", | |
| "- seg_5_PLPE 2454 PLPE C34 C35 | seg_2_CHL1 1970 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2331 POPC C213 C214 | seg_2_CHL1 1978 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_4_POPC 2372 POPC C36 C37 | seg_2_CHL1 1982 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2623 PLPC C215 C216 | seg_2_CHL1 1983 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2881 PLPA C310 C311 | seg_2_CHL1 1992 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_9_PLPA 2879 PLPA C212 C213 | seg_2_CHL1 1997 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2604 PLPC C212 C213 | seg_2_CHL1 1998 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2166 PLPI C311 C312 | seg_2_CHL1 2001 CHL1 C6 C7 C8 C9 C10 C5\n", | |
| "- seg_6_PLPC 2523 PLPC C26 C27 | seg_2_CHL1 2009 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_6_PLPC 2523 PLPC C215 C216 | seg_2_CHL1 2009 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2601 PLPC C28 C29 | seg_2_CHL1 2014 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_8_POPA 2825 POPA C25 C26 | seg_2_CHL1 2017 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_9_PLPA 2869 PLPA C26 C27 | seg_2_CHL1 2019 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2589 PLPC C310 C311 | seg_2_CHL1 2027 CHL1 C14 C15 C16 C17 C13\n", | |
| "- seg_6_PLPC 2564 PLPC C315 C316 | seg_2_CHL1 2027 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_6_PLPC 2532 PLPC C216 C217 | seg_2_CHL1 2028 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_5_PLPE 2404 PLPE C313 C314 | seg_2_CHL1 2036 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_POPC 2270 POPC O21 C21 | seg_2_CHL1 2041 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_3_PLPI 2186 PLPI C315 C316 | seg_2_CHL1 2042 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_9_PLPA 2861 PLPA C25 C26 | seg_2_CHL1 2048 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_6_PLPC 2598 PLPC C210 C211 | seg_2_CHL1 2062 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_3_PLPI 2123 PLPI C215 C216 | seg_2_CHL1 2066 CHL1 C16 C15 C14 C13 C17\n", | |
| "- seg_6_PLPC 2564 PLPC C213 C214 | seg_2_CHL1 2069 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_4_POPC 2334 POPC C35 C36 | seg_2_CHL1 2070 CHL1 C5 C4 C3 C2 C1 C10\n", | |
| "- seg_4_POPC 2334 POPC C39 C310 | seg_2_CHL1 2070 CHL1 C14 C8 C9 C11 C12 C13\n", | |
| "- seg_6_PLPC 2637 PLPC C39 C310 | seg_2_CHL1 2084 CHL1 C6 C5 C10 C9 C8 C7\n", | |
| "- seg_6_PLPC 2569 PLPC C36 C37 | seg_2_CHL1 2089 CHL1 C8 C7 C6 C5 C10 C9\n", | |
| "- seg_6_PLPC 2541 PLPC C211 C212 | seg_2_CHL1 2112 CHL1 C5 C6 C7 C8 C9 C10\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem_prob.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem_prob.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 36, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n" | |
| ] | |
| }, | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "<ipython-input-5-5b658d4b0d49>:17: RuntimeWarning: divide by zero encountered in true_divide\n", | |
| " n = -np.array((v[i,0], v[i,1], d))/v[i,2]\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem_chl1.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_NOPNU_EPJ_SLIPIDS/alchembed/alchem_chl1.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 38, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n", | |
| "found a ring penetration:\n", | |
| "- seg_16_PNU 153732 PNU C6 C12 | seg_4_CHL1 1970 CHL1 C14 C15 C16 C17 C13\n", | |
| "- seg_16_PNU 153732 PNU C1 N1 | seg_4_CHL1 1970 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_16_PNU 153732 PNU C2 N2 | seg_4_CHL1 1970 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_16_PNU 153732 PNU O2 C3 | seg_4_CHL1 1970 CHL1 C3 C4 C5 C10 C1 C2\n", | |
| "- seg_16_PNU 153734 PNU C1 N1 | seg_4_CHL1 1980 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_16_PNU 153728 PNU C1 N1 | seg_4_CHL1 2042 CHL1 C8 C14 C13 C12 C11 C9\n", | |
| "- seg_16_PNU 153728 PNU C2 C5 | seg_4_CHL1 2042 CHL1 C5 C6 C7 C8 C9 C10\n", | |
| "- seg_16_PNU 153728 PNU N2 O2 | seg_4_CHL1 2042 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_16_PNU 153734 PNU C3 C4 | seg_4_CHL1 2123 CHL1 C4 C5 C10 C1 C2 C3\n", | |
| "- seg_4_CHL1 2042 CHL1 C5 C10 | seg_16_PNU 153728 PNU N2 O2 C3 C5 C2\n", | |
| "- seg_4_CHL1 1970 CHL1 C15 C16 | seg_16_PNU 153732 PNU C7 C8 C9 C11 C12 C6\n", | |
| "- seg_4_CHL1 1970 CHL1 C5 C10 | seg_16_PNU 153732 PNU N2 O2 C3 C5 C2\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_PNU_EPJ_SLIPIDS/em.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_PNU_EPJ_SLIPIDS/em.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 41, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "In frame 0\n", | |
| "%lipid ring pentration\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "universe = mda.Universe('./SIMULATIONS/NACHRA7_PNU_EPJ_SLIPIDS/alchem.tpr',\n", | |
| " './SIMULATIONS/NACHRA7_PNU_EPJ_SLIPIDS/alchem.gro')\n", | |
| "check_universe_ring_penetration(universe)" | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "mda_py38", | |
| "language": "python", | |
| "name": "jupyter" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.8.0" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 4 | |
| } |
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