{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"# PyGromos File Examples"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"import os, sys\n",
"root_dir = os.getcwd()\n",
"\n",
"#if package is not installed and path not set correct - this helps you out :)\n",
"sys.path.append(root_dir+\"/..\")"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"## IMD - Simulation Paramter File"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from pygromos.files.simulation_parameters.imd import Imd\n",
"\n",
"#load template IMD - simulation parameter filess\n",
"from pygromos.data.simulation_parameters_templates import template_md\n",
"imd = Imd(template_md)\n",
"\n",
"#change number of simulation steps and Temperatures\n",
"imd.STEP.NSTLIM = 500\n",
"print(imd.STEP)\n",
"\n",
"simulation_temperature = 420\n",
"imd.MULTIBATH.TEMP0 = [simulation_temperature for x in range(imd.MULTIBATH.NBATHS)]\n",
"print(imd.MULTIBATH)\n",
"\n",
"\n",
"#store file\n",
"out_imd_path=\"./test.imd\"\n",
"out_imd = imd.write(out_imd_path)"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"## CNF - Coordinate File"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from pygromos.files.coord import Cnf\n",
"\n",
"in_cnf=\"../example_files/MD_Simulation/MD_input/in_md.cnf\"\n",
"\n",
"cnf = Cnf(in_cnf)\n",
"\n",
"#print(cnf.residues) #noisy\n",
"cnf.view"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Deleting Residues"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"[ cnf.delete_residue(resID=x) for x in range(1,3)]\n",
"cnf.view"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Generate position Restraint Files"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"restraint_residues = [k for k in cnf.residues if (k!= \"SOLV\")]\n",
"posres_file = cnf.gen_possrespec(residues=restraint_residues)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"refpos_file = cnf.gen_refpos()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Compact all"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"\"\"\"\n",
" CNF\n",
"\"\"\"\n",
"from pygromos.files.coord import Cnf\n",
"from pygromos.tests import in_testfiles\n",
"#load_cnf\n",
"in_cnf= in_testfiles.in_test_file_path+\"/cnf/in_cnf1.cnf\"\n",
"out_cnf=\"../example_files/new.cnf\"\n",
"\n",
"cnf = Cnf(in_cnf)\n",
"\n",
"#get residues of cnf\n",
"residues = cnf.get_residues()\n",
"\n",
"#Delete Residues\n",
"delete_ligands = [\"delete ME!\"]\n",
"for resn in delete_ligands:\n",
" cnf.delete_residue(resName=resn)\n",
"\n",
"#set new title\n",
"lig_sys = [\"lig1\", \"lig2\", \"lig3\"]\n",
"cnf.TITLE.content = \" Ligands:\\t \" + \" \".join(lig_sys) + \"\\n\"\n",
"\n",
"#cleaning\n",
"cnf.clean_posiResNums()\n",
"\n",
"#get_file content:\n",
"#print(cnf) #a lot of output ;)\n",
"\n",
"#store again\n",
"out_cnf = cnf.write(out_path=out_cnf)"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
},
"tags": []
},
"source": [
"## TOP - Topology File\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from pygromos.files.topology import top\n",
"from pygromos.tests import in_testfiles\n",
"\n",
"top_file_path = in_testfiles.in_test_file_path+\"/top/test.top\"\n",
"top_file = top.Top(top_file_path)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"top_file.SOLUTEMOLECULES\n",
"#top_file.SOLUTEATOM #noisy :)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## TRC - Coordinate Trajectory File"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import glob\n",
"from pygromos.files.trajectory.trc import Trc"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"trc_file = Trc(traj_path='../example_files/Traj_files/b_emin_vacuum_1.trc',\n",
" in_cnf='../example_files/Traj_files/b_emin_vacuum.cnf')\n",
"print(trc_file)\n",
"\n",
"trc_file.view"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"## Other Files\n",
"\n",
"### MTB - topology building block file\n",
"\n",
" **to be implemented!**\n",
" \n",
"### IFP - topology parameter file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"\n",
"from pygromos.files.topology import ifp\n",
"from pygromos.data.ff import Gromos54A7\n",
"\n",
"#parse forcefield file\n",
"myfp = ifp.Ifp(Gromos54A7.ifp)\n",
"myfp.write(os.getcwd()+\"/fun.ifp\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"#parse output and write out again\n",
"test = ifp.Ifp(os.getcwd()+\"/fun.ifp\")\n",
"test"
]
},
{
"cell_type": "markdown",
"metadata": {
"pycharm": {
"name": "#%% md\n"
}
},
"source": [
"### disres - distance restraint file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"from pygromos.files.topology import disres\n",
"from pygromos.tests import in_testfiles\n",
"\n",
"disres_file_path = in_testfiles.in_test_file_path+\"/top/disres5.disres\"\n",
"disres_file = disres.Disres(disres_file_path)\n",
"disres_file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"print(\"\\t\".join(disres_file.DISTANCERESSPEC.RESTRAINTHEADER))\n",
"print(disres_file.DISTANCERESSPEC.RESTRAINTS[0])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## PTP - Pertubations for free energy calculations\n",
"\n",
"Here I try to give a few example on what s possible with the ptp obj in pygromos."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"from pygromos.files.topology.ptp import Pertubation_topology as PTP\n",
"from pygromos.files.blocks.pertubation_blocks import MPERTATOM, atom_eds_pertubation_state, pertubation_eds_state\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### defining some state types for later use :)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"dummy_type = pertubation_eds_state(IAC=22, CHARGE=0.0)\n",
"my_type = pertubation_eds_state(IAC=99, CHARGE=-1.0)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Read in ptp file"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"#Read in ptp file:\n",
"from pygromos.tests import in_testfiles\n",
"\n",
"path= in_testfiles.in_test_file_path+\"/ptp/eds_short.ptp\"\n",
"ptp = PTP(path)\n",
"print(ptp)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### delete full state"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"ptp.MPERTATOM.delete_state(stateIDs=[1,3])\n",
"\n",
"print(ptp)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### delete specific atoms"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"ptp.MPERTATOM.delete_atom(atomNR=[1,2,7,8,9])\n",
"print(ptp)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Add atom or state or overwrite atominformation (except atom.NR)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"pycharm": {
"name": "#%%\n"
}
},
"outputs": [],
"source": [
"numStates=1\n",
"new_atoms_state = [atom_eds_pertubation_state(NR=x, NAME=\"H\", STATES={7: my_type}) for x in range(1, 4+1)]\n",
"ptp.add_block(block=MPERTATOM(NJLA=len(new_atoms_state), NPTB=numStates, STATEATOMS=new_atoms_state))\n",
"\n",
"print(ptp)"
]
}
],
"metadata": {
"interpreter": {
"hash": "b1b7b2ea43b8e767316eee98e01335d045804d2d47db68b6a5827e187ee91a7e"
},
"kernelspec": {
"display_name": "pygro2",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
}
},
"nbformat": 4,
"nbformat_minor": 4
}