def extract_docking_results(self, file_s, input_file_r, input_file_l):
subprocess.check_output(license.wrap_command(
"moebatch -exec \"db_ExportTriposMOL2 ['dock.mdb', 'lig.mol2', 'mol', []]\"",
'moe'),
shell=True,
executable='/bin/bash')
if os.path.exists('lig.mol2'):
ligname = reader.open(input_file_l).ligname
mol2.update_mol2file('lig.mol2',
'lig-.mol2',
ligname=ligname,
multi=True)
os.remove('lig.mol2')
# get SDF to extract scores
sdffile = 'lig.sdf'
subprocess.check_output(license.wrap_command(
"moebatch -exec \"db_ExportSD ['dock.mdb', '%s', ['mol','S'], []]\""
% sdffile, 'moe'),
shell=True,
executable='/bin/bash')
with open(sdffile, 'r') as sdff:
with open(file_s, 'w') as sf:
for line in sdff:
if line.startswith("> <S>"):
print >> sf, sdff.next().strip()
os.remove(sdffile)
else:
open(file_s, 'w').close()
def write_rescoring_script(self, filename, file_r, files_l):
"""Rescore using Glide SP scoring function"""
locals().update(self.options)
files_l_joined = ' '.join(files_l)
if self.use_prepwizard:
# prepare protein cmd (the protein structure is already assumed to be minimized/protonated with prepwizard)
prepwizard_cmd = license.wrap_command(
"prepwizard -fix %(file_r)s target.mae" % locals(),
'schrodinger')
else:
prepwizard_cmd = "structconvert -ipdb %(file_r)s -omae target.mae" % locals(
)
# prepare grid and scoring cmd
glide_grid_cmd = license.wrap_command("glide grid.in",
'schrodinger') # grid prepare
glide_dock_cmd = license.wrap_command("glide dock.in",
'schrodinger') # docking command
tmpdirline = self.tmpdirline
with open(filename, 'w') as file:
script = """#!/bin/bash
%(tmpdirline)s
cat %(files_l_joined)s > lig.mol2
# (A) Prepare receptor
%(prepwizard_cmd)s
# (B) Prepare grid
echo "USECOMPMAE YES
INNERBOX %(innerbox)s
ACTXRANGE %(actxrange)s
ACTYRANGE %(actyrange)s
ACTZRANGE %(actzrange)s
GRID_CENTER %(grid_center)s
OUTERBOX %(outerbox)s
ENTRYTITLE target
GRIDFILE grid.zip
RECEP_FILE target.mae" > grid.in
%(glide_grid_cmd)s
# (C) convert ligand to maestro format
structconvert -imol2 lig.mol2 -omae lig.mae
# (D) perform rescoring
echo "WRITEREPT YES
USECOMPMAE YES
DOCKING_METHOD inplace
GRIDFILE $PWD/grid.zip
LIGANDFILE $PWD/lig.mae
PRECISION SP" > dock.in
%(glide_dock_cmd)s""" % locals()
file.write(script)
def write_docking_script(self, filename, file_r, file_l):
""" Write docking script for glide """
locals().update(self.options)
if self.use_prepwizard:
# prepare protein cmd (the protein structure is already assumed to be minimized/protonated with prepwizard)
prepwizard_cmd = license.wrap_command(
"prepwizard -fix %(file_r)s target.mae" % locals(),
'schrodinger')
else:
prepwizard_cmd = "structconvert -ipdb %(file_r)s -omae target.mae" % locals(
)
# prepare grid and docking cmd
glide_grid_cmd = license.wrap_command("glide grid.in", 'schrodinger')
glide_dock_cmd = license.wrap_command("glide dock.in", 'schrodinger')
tmpdirline = self.tmpdirline
# write glide script
with open(filename, 'w') as file:
script = """#!/bin/bash
%(tmpdirline)s
# (A) Prepare receptor
%(prepwizard_cmd)s
# (B) Prepare grid
echo "USECOMPMAE YES
INNERBOX %(innerbox)s
ACTXRANGE %(actxrange)s
ACTYRANGE %(actyrange)s
ACTZRANGE %(actzrange)s
GRID_CENTER %(grid_center)s
OUTERBOX %(outerbox)s
ENTRYTITLE target
GRIDFILE grid.zip
RECEP_FILE target.mae" > grid.in
%(glide_grid_cmd)s
# (C) convert ligand to maestro format
structconvert -imol2 %(file_l)s -omae lig.mae
# (D) perform docking
echo "WRITEREPT YES
USECOMPMAE YES
DOCKING_METHOD confgen
POSES_PER_LIG %(poses_per_lig)s
POSE_RMSD %(pose_rmsd)s
GRIDFILE $PWD/grid.zip
LIGANDFILE $PWD/lig.mae
PRECISION %(precision)s" > dock.in
%(glide_dock_cmd)s""" % locals()
file.write(script)
def write_sitefinder_script(filename, file_r, args):
write_moe_sitefinder_script('sitefinder.svl', file_r, args)
sitefinder_cmd = license.wrap_command("moebatch -run sitefinder.svl",
'moe') # cmd for docking
# write script
with open(filename, 'w') as file:
script = """#!/bin/bash
# run docking
%(sitefinder_cmd)s
""" % locals()
file.write(script)
def write_docking_script(self, filename, file_r, file_l):
self.write_moe_docking_script('moe_dock.svl')
convertmol2_cmd = license.wrap_command(
"moebatch -exec \"mdb_key = db_Open ['ligand.mdb','create']; db_Close mdb_key;\
db_ImportMOL2 ['%(file_l)s','ligand.mdb', 'molecule']\"" % locals(),
'moe') # create mdb for ligand
dock_cmd = license.wrap_command(
"moebatch -run moe_dock.svl -rec %(file_r)s -lig ligand.mdb" %
locals(), 'moe') # cmd for docking
# write script
with open(filename, 'w') as ff:
script = """#!/bin/bash
# convert .mol2 file to mdb
%(convertmol2_cmd)s
# run docking
%(dock_cmd)s\n""" % locals()
ff.write(script)
def extract_rescoring_results(self, file_s):
locals().update(self.options)
if self.options['rescoring'] == 'prolig':
with open(file_s, 'a') as sf:
if os.path.exists('moebatch.log'):
with open('moebatch.log', 'r') as logf:
is_interaction_energy = False
for line in logf:
if line.startswith("Interaction energy:"):
print >> sf, line.split()[-2]
is_interaction_energy = True
break
if not is_interaction_energy:
print >> sf, 'NaN'
else:
print >> sf, 'NaN'
else:
# get SDF to extract scores
sdffile = 'lig.sdf'
subprocess.check_output(license.wrap_command(
"moebatch -exec \"db_ExportSD ['dock.mdb', '%s', ['mol','S'], []]\""
% sdffile, 'moe'),
shell=True,
executable='/bin/bash')
with open(file_s, 'a') as sf:
if os.path.exists(sdffile):
with open(sdffile, 'r') as sdff:
for line in sdff:
if line.startswith("> <S>"):
print >> sf, sdff.next().strip()
break
os.remove(sdffile)
else:
print >> sf, 'NaN'
def write_docking_script(self, filename, file_r, file_l):
locals().update(self.options)
dock_cmd = license.wrap_command("gold_auto gold.conf",
'gold') # cmd for docking
# write autodock script
with open(filename, 'w') as file:
script = """#!/bin/bash
echo " GOLD CONFIGURATION FILE
AUTOMATIC SETTINGS
autoscale = 0.5
POPULATION
popsiz = auto
select_pressure = auto
n_islands = auto
maxops = auto
niche_siz = auto
GENETIC OPERATORS
pt_crosswt = auto
allele_mutatewt = auto
migratewt = auto
FLOOD FILL
radius = %(radius)s
origin = %(origin)s
do_cavity = 1
floodfill_atom_no = 0
cavity_file =
floodfill_center = point
DATA FILES
ligand_data_file %(file_l)s %(nposes)s
param_file = DEFAULT
set_ligand_atom_types = 1
set_protein_atom_types = 0
directory = .
tordist_file = DEFAULT
make_subdirs = 0
save_lone_pairs = 1
fit_points_file = f it_pts.mol2
read_fitpts = 0
FLAGS
internal_ligand_h_bonds = 0
flip_free_corners = 0
match_ring_templates = 0
flip_amide_bonds = 0
flip_planar_n = 1 flip_ring_NRR flip_ring_NHR
flip_pyramidal_n = 0
rotate_carboxylic_oh = flip
use_tordist = 1
postprocess_bonds = 1
rotatable_bond_override_file = DEFAULT
solvate_all = 1
TERMINATION
early_termination = 1
n_top_solutions = 3
rms_tolerance = 1.5
CONSTRAINTS
force_constraints = 0
COVALENT BONDING
covalent = 0
SAVE OPTIONS
save_score_in_file = 1
save_protein_torsions = 1
FITNESS FUNCTION SETTINGS
initial_virtual_pt_match_max = 3
relative_ligand_energy = 1
gold_fitfunc_path = goldscore
start_vdw_linear_cutoff = 6
score_param_file = DEFAULT
PROTEIN DATA
protein_datafile = %(file_r)s" > gold.conf
%(dock_cmd)s""" % locals()
file.write(script)
def write_rescoring_script(self, filename, file_r, file_l):
locals().update(self.options)
if self.options['rescoring'] == 'prolig':
rescoring_cmd = license.wrap_command(
"moebatch -run moe_rescoring.svl -rec %(file_r)s -lig %(file_l)s"
% locals(), 'moe') # cmd for docking
with open(filename, 'w') as file:
script = """#!/bin/bash
echo "#svl
function prolig_Calculate;
global argv;
function ArgvPull;
local function main[]
ArgvReset ArgvExpand argv;
local [recmdb, ligmdb, outf] = ArgvPull [
['-rec','-lig','-o'],
1
];
local lk = ReadTriposMOL2 [ligmdb, []];
// Load pdb
local rk = ReadAuto [recmdb, []];
local itypes = ['hbond', 'metal', 'ionic', 'covalent', 'arene', 'distance'];
local iract = prolig_Calculate [itypes, lk, rk, []];
//local iract_v = Formulate2DInteractions [lk, rk, []];
local idx;
local interaction_energy = 0.;
for idx = 1, length iract(1) loop
if iract(1)(idx) == 'distance' then
break;
else
interaction_energy = interaction_energy + iract(4)(idx);
endif
endloop
write ['Interaction energy: {f.2} kCal/mol \\n', interaction_energy];
endfunction;" > moe_rescoring.svl
%(rescoring_cmd)s
""" % locals()
file.write(script)
else:
convertmol2_cmd = license.wrap_command(
"moebatch -exec \"mdb_key = db_Open ['lig.mdb','create']; db_Close mdb_key;\
db_ImportMOL2 ['%(file_l)s','lig.mdb', 'molecule']\"" % locals(),
'moe') # create mdb for ligand
rescoring_cmd = license.wrap_command(
"moebatch -run moe_rescoring.svl -rec %(file_r)s -lig lig.mdb"
% locals(), 'moe') # cmd for docking
# write vina script
with open(filename, 'w') as file:
script = """#!/bin/bash
%(convertmol2_cmd)s
echo "#svl
function DockAtoms, DockFile;
function DockMDBwAtoms, DockMDBwFile;
global argv;
function ArgvPull;
local function main []
// Set potential and setup parameters
pot_Load '$MOE/lib/Amber10EHT.ff';
pot_Setup [
strEnable: 1,
angEnable: 1,
stbEnable: 1,
oopEnable: 1,
torEnable: 1,
vdwEnable: 1,
eleEnable: 1,
solEnable: 0,
resEnable: 1,
strWeight: 1,
angWeight: 1,
stbWeight: 1,
oopWeight: 1,
torWeight: 1,
vdwWeight: 1,
eleWeight: 1,
solWeight: 1,
resWeight: 1,
cutoffEnable: 1,
cutoffOn: 8,
cutoffOff: 10,
eleDist: 2,
vdwScale14: 0.5,
vdwBuffer1: 0,
vdwBuffer2: 0,
eleScale14: 0.833333,
eleDielectric: 1,
eleBuffer: 0,
solDielectric: 80,
solDielectricOffset: 0,
state0: 1,
state1: 0,
state2: 1,
threadCount: 0
];
ArgvReset ArgvExpand argv;
local [recmdb, ligmdb, ph4file, outf] = ArgvPull [
['-rec','-lig','-ph4','-o'],
1
];
// If no receptor given as argument use default rec.moe
if isnull recmdb then
recmdb = 'rec.moe';
endif
local basename = fbase recmdb;
local extension = fext recmdb;
// output docking database file
outf = 'dock.mdb';
// Receptor file or database
// Assume that the file is a moe or pdb file extract chains atoms
local chains = ReadAuto [recmdb, []];
local rec = cat cAtoms chains; // extract atom info from atom
local alpha_sites = run['sitefind.svl', [rec, []], 'AlphaSites'];
// Take first/highest scoring pocket alpha_sites(1)
// Take fpos data alpha_sites(1)(1)
// Take only coords of fpos data alpha_sites(1)(1)(2)
local a_sites = apt cat alpha_sites(1)(1)(2); // x, y, z coords
// Make dummy He atoms for alpha site
local dummy, x, y, z;
for x = 1, length a_sites loop
dummy(x) = sm_Build ['[He]'];
aSetPos [dummy(x), a_sites(x)];
endloop
// Make a collection of site atoms to send to docking
// from the alpha site
oSetCollection ['Site', dummy];
local site = oGetCollection 'Site';
// Ligand database
local lmdb = _db_Open [ligmdb, 'read'];
if lmdb == 0 then
exit twrite ['Cannot read ligand mdb file {}', ligmdb];
endif
local ent = 0; // must have this set to zero
while ent = db_NextEntry[lmdb, ent] loop; //loop through ligand database
local ligdata = db_Read[lmdb, ent]; //read data for each entry
local ligmoldata = ligdata.mol; // extract into moldata
local ligchains = mol_Create ligmoldata; //create molecule in window
local lig = cat cAtoms ligchains; // extract atom info from atom
endloop
// Set options for docking and refinement
// maxpose is set to accept 50 poses, change as required
local opt = [
outrmsd: 1,
sel_ent_only_rec: 0,
sel_ent_only: 0,
wall: [ '', 0, [ 0, 0, 0 ], [ 1000000, 1000000, 1000000 ], 0 ],
csearch: 1,
placement: 'None',
scoring: 'None',
dup_placement: 1,
rescoring: '%(rescoring)s',
rescoring_opt: [ train : 0 ],
dup_refine: 1,
remaxpose: 1,
descexpr: '',
receptor_mfield: '',
ligand_mfield: '',
tplate: [ ],
tplateSel: [ ],
ligmdbname: ligmdb,
recmdbname: recmdb
];
//Perform the docking
DockFile [rec, site, ligmdb, outf, opt];
oDestroy ligchains;
db_Close lmdb;
write ['Docking finished at {}.\\n', asctime []];
endfunction;" > moe_rescoring.svl
%(rescoring_cmd)s""" % locals()
file.write(script)