def compute_mcss(self, ligands, init_file, mcss_types_file, small=False):
"""
Compute the MCSS file by calling Schrodinger canvasMCSS.
Updates instance with MCSSs present in the file
"""
structure_file = '{}.ligands.mae'.format(init_file)
mcss_file = '{}.mcss.csv'.format(init_file)
stwr = StructureWriter(structure_file)
stwr.append(ligands[self.l1])
stwr.append(ligands[self.l2])
stwr.close()
# set the sizes in atoms of each of the ligands
self._set_ligand_sizes(structure_file)
if os.system(
self.mcss_cmd.format(structure_file, mcss_file,
5 if small else 10, mcss_types_file)):
assert False, 'MCSS computation failed'
self._set_mcss(mcss_file)
self.tried_small = small
with open(init_file, 'a+') as fp:
fp.write(str(self) + '\n')
os.system('rm {} {}'.format(structure_file, mcss_file))
def save_merged_ligand_protein(self, raw_protein_file, raw_ligand_file):
"""
Merge structures from files and save to save directory
:param raw_ligand_file: absolute paths
:return:
"""
prot_st = next(StructureReader(raw_protein_file))
alpha = 'ABCDEFGHIJKMNOPQRST'
alpha_count = 0
for c in prot_st.chain:
if c.name.strip() == '': continue
c.name = alpha[alpha_count]
alpha_count += 1
if raw_ligand_file != '':
lig_st = next(StructureReader(raw_ligand_file))
# standardize chain naming
for c in lig_st.chain:
c.name = 'L'
merged_st = lig_st.merge(prot_st)
else:
merged_st = prot_st
st_wr = StructureWriter(self.path + self.raw_complex)
st_wr.append(merged_st)
st_wr.close()
def split(self):
#look for the opt_complex, if it doesn't exist, just use the prepped complex
usefile = ''
if (os.path.isfile(self.path + self.align_file)):
usefile = self.path + self.align_file
else:
usefile = self.path + self.prepped_complex
st = next(StructureReader(usefile))
prot_st = st.extract([a.index for a in st.atom if a.chain != 'L'])
prot_st.title = '{}_prot'.format(self.name)
lig_st = st.extract([a.index for a in st.atom if a.chain == 'L'])
lig_st.title = '{}_lig'.format(self.name)
prot_wr = StructureWriter(self.path + self.split_protein)
prot_wr.append(prot_st)
prot_wr.close()
lig_wr = StructureWriter(self.path + self.split_ligand)
lig_wr.append(lig_st)
lig_wr.close()
"""
The purpose of this code is to remove the ligands from a list of structure (.mae) files
It can be run on sherlock using
$ ml load chemistry
$ ml load schrodinger
$ $SCHRODINGER/run python3 ligand_remover.py
"""
import os
from schrodinger.structure import StructureReader, StructureWriter
if __name__ == '__main__':
root = '/home/users/sidhikab/flexibility_project/mutations/Data/MAPK14/'
files = sorted(os.listdir(root))
for s_file in files:
if len(s_file) == 16:
print(s_file)
prot_path = s_file[:12] + '_nolig.mae'
if os.path.exists(root + prot_path):
print("Exists")
else:
st = next(StructureReader(root + s_file))
prot_st = st.extract(
[a.index for a in st.atom if a.chain != 'L'])
prot_wr = StructureWriter(root + prot_path)
prot_wr.append(prot_st)
prot_wr.close()
os.remove(root + s_file)