A series of Python3 script to lower the barrier of computing and simulating molecular and material systems.
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import os
def readpdb(geom):
others = []
ligands = []
water = []
with open(geom, 'r') as f:
for line in f:
if line.startswith('HETATM'):
others.append(line.strip())
for i in others:
if 'HOH' in i:
water.append(i)
else:
ligands.append(i)
ligandname = []
for i in ligands:
ligandname.append(i.split()[3])
ligandname = set(ligandname)
print("File pdb ini mengandung {} ligan, yaitu:".format(len(ligandname)))
for i in ligandname:
print(i)
def splitpdb(geom,ligname):
ligand = []
with open(geom, 'r') as f:
for line in f:
if line.startswith('ATOM' or 'TER'):
protein.append(line.strip())
if 'HETATM' in line:
if "{}".format(ligname) in line:
ligand.append(line.strip())
with open('lig_{}.pdb'.format(ligname),'w') as f:
for i in ligand:
print(i,file=f)
## Jangan lakukan addH dan addcharge untuk molekul protein, ini khusus untuk molekul-molekul organik kecil. Untuk protein, gunakan Chimera!
def addH(geom):
arr = geom.split(".")
filename = arr[0]
os.system("obabel {} -p 7.4 -O {}_withH.pdb".format(geom,filename))
def addcharge(geom,chargetype):
arr = geom.split(".")
filename = arr[0]
os.system("obabel {} --partialcharge {} -O {}.mol2".format(geom,chargetype,filename))
def sphgen(geom):
os.system("$DMS_COMMAND {} -n -w 1.4 -v -o protein.ms".format(geom))
with open('INSPH','w') as f:
print("""protein.ms
R
X
0.0
4
1.4
protein.sph""",file=f)
if os.path.exists('OUTSPH'):
os.remove('OUTSPH')
if os.path.exists('protein.sph'):
os.remove('protein.sph')
# os.system("$DOCK_DIR/sphgen")
# os.system("$DOCK_DIR/sphere_selector protein.sph {} 10".format(ligname))
def showsphere():
with open('selected_spheres.in','w') as f:
print("""selected_spheres.sph
1
N
selected_spheres.pdb
""",file=f)
os.system('$DOCK_DIR/showsphere < selected_spheres.in')
def gridgen(geom):
os.system('cp $DOCK_PARM/vdw_AMBER_parm99.defn .')
with open('box.in','w') as f:
print("""Y
5
selected_spheres.sph
1
protein_box.pdb
""",file=f)
os.system('$DOCK_DIR/showbox < box.in')
with open('grid.in','w') as f:
print("""compute_grids yes
grid_spacing 0.3
output_molecule no
contact_score no
energy_score yes
energy_cutoff_distance 9999
atom_model a
attractive_exponent 6
repulsive_exponent 12
distance_dielectric yes
dielectric_factor 4
bump_filter yes
bump_overlap 0.75
receptor_file {}
box_file protein_box.pdb
vdw_definition_file vdw_AMBER_parm99.defn
score_grid_prefix grid
""".format(geom),file=f)
# os.system('$DOCK_DIR/grid -i grid.in')
def rigiddock(ligname,rmsd):
arr = ligname.split(".")
filename = arr[-2]
if os.path.exists('RigidDock_{}'.format(filename)):
os.system('rm -rf RigidDock_{}'.format(filename))
os.mkdir('RigidDock_{}'.format(filename))
os.chdir('RigidDock_{}'.format(filename))
os.system('cp $DOCK_PARM/flex.defn .')
os.system('cp $DOCK_PARM/flex_drive.tbl .')
with open('rigid.in','w') as f:
print("""conformer_search_type rigid
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file ../{}
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd {}
use_database_filter no
orient_ligand yes
automated_matching yes
receptor_site_file ../selected_spheres.sph
max_orientations 1000
critical_points no
chemical_matching no
use_ligand_spheres no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary yes
grid_score_secondary no
grid_score_rep_rad_scale 1
grid_score_vdw_scale 1
grid_score_es_scale 1
grid_score_grid_prefix ../grid
multigrid_score_secondary no
dock3.5_score_secondary no
continuous_score_secondary no
footprint_similarity_score_secondary no
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand yes
simplex_max_iterations 1000
simplex_tors_premin_iterations 0
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_random_seed 0
simplex_restraint_min no
atom_model all
vdw_defn_file ../vdw_AMBER_parm99.defn
flex_defn_file flex.defn
flex_drive_file flex_drive.tbl
ligand_outfile_prefix rigid
write_orientations no
num_scored_conformers 1
rank_ligands no
""".format(ligname,rmsd),file=f)
# os.system('$DOCK_DIR/dock6 -i rigid.in -o rigid.out')
def flexdock(ligname,rmsd):
arr = ligname.split(".")
filename = arr[-2]
if os.path.exists('FlexDock_{}'.format(filename)):
os.system('rm -rf FlexDock_{}'.format(filename))
os.mkdir('FlexDock_{}'.format(filename))
os.chdir('FlexDock_{}'.format(filename))
os.system('cp $DOCK_PARM/flex.defn .')
os.system('cp $DOCK_PARM/flex_drive.tbl .')
with open('flex.in','w') as f:
print("""conformer_search_type flex
write_fragment_libraries no
user_specified_anchor no
limit_max_anchors no
min_anchor_size 40
pruning_use_clustering yes
pruning_max_orients 100
pruning_clustering_cutoff 100
pruning_conformer_score_cutoff 25.0
pruning_conformer_score_scaling_factor 1.0
use_clash_overlap no
write_growth_tree no
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file ../{}
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd {}
use_database_filter no
orient_ligand yes
automated_matching yes
receptor_site_file ../selected_spheres.sph
max_orientations 500
critical_points no
chemical_matching no
use_ligand_spheres no
bump_filter no
score_molecules yes
contact_score_primary no
contact_score_secondary no
grid_score_primary yes
grid_score_secondary no
grid_score_rep_rad_scale 1
grid_score_vdw_scale 1
grid_score_es_scale 1
grid_score_grid_prefix ../grid
multigrid_score_secondary no
dock3.5_score_secondary no
continuous_score_secondary no
footprint_similarity_score_secondary no
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_score_secondary no
amber_score_secondary no
minimize_ligand yes
minimize_anchor yes
minimize_flexible_growth yes
use_advanced_simplex_parameters no
simplex_max_cycles 1
simplex_score_converge 0.1
simplex_cycle_converge 1.0
simplex_trans_step 1.0
simplex_rot_step 0.1
simplex_tors_step 10.0
simplex_anchor_max_iterations 1000
simplex_grow_max_iterations 1000
simplex_grow_tors_premin_iterations 0
simplex_random_seed 0
simplex_restraint_min no
atom_model all
vdw_defn_file ../vdw_AMBER_parm99.defn
flex_defn_file flex.defn
flex_drive_file flex_drive.tbl
ligand_outfile_prefix flex
write_orientations no
num_scored_conformers 1
rank_ligands no
""".format(ligname,rmsd),file=f)
# os.system('$DOCK_DIR/dock6 -i flex.in -o flex.out')
def translig(ligand):
arr = ligand.split(".")
filename = arr[-2]
os.system("obabel {} -O {}_center.xyz -c".format(ligand,filename))
center_x = 0
center_y = 0
center_z = 0
with open('protein_box.pdb','r') as f:
for line in f:
if 'CENTER' in line:
arr = line.split()
center_x+=float(arr[5])
center_y+=float(arr[6])
center_z+=float(arr[7])
os.system("$DOCK_DIR/transform.py {}_center.xyz -tx {} -ty {} -tz {} > {}_trans.xyz".format(filename,center_x,center_y,center_z,filename))
os.system('obabel {}_trans.xyz -O {}.pdb'.format(filename,filename))
os.system('rm {}_center.xyz'.format(filename))
os.system('rm {}_trans.xyz'.format(filename))
def sdf2xyz(ligand):
with open('run_babel.sh','w') as fout:
with open('run_babel.sh','w') as fout:
print("""#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=168:0:0
cd $PWD
obabel {} -O lig.xyz -m""".format(ligand),file=fout)
os.system('sbatch run_babel.sh')
def multiopt(nligands):
for i in range(1,nligands+1):
os.system('mkdir lig{}'.format(i))
os.system('cp lig{}.xyz lig{}'.format(i,i))
os.chdir('lig{}'.format(i))
os.system('cmmde.py -s dcdftb -j opt -i lig{}.xyz -m DFTB3 -disp D3BJ -np 2 -solvent water'.format(i))
os.chdir('../')
def checkopt(nligands):
for i in range(1,nligands+1):
os.chdir('lig{}'.format(i))
with open('cmmd.out','r') as f:
for line in f:
if "Stationary point found" in line:
print("Optimasi geometri lig{} sukses!!!".format(i))
os.chdir('../')
def multiflexdock(nligands,chargetype):
for i in range(1,nligands+1):
os.chdir('lig{}'.format(i))
os.system('cmmdepost.py -s dcdftb -j opt -i lig{}.xyz'.format(i))
os.system('cp ../protein_box.pdb .')
os.system('cmmde.py -s dock -j translig -ligand cmmd.xyz')
os.system('rm protein_box.pdb')
os.system('cmmde.py -s dock -j addcharge -i cmmd.pdb -chargetype {}'.format(chargetype))
os.system('cp cmmd.mol2 ../lig{}.mol2'.format(i))
os.chdir('../')
os.system('cmmde.py -s dock -j flexdock -ligand lig{}.mol2'.format(i))