Exemple #1
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    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))
Exemple #2
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    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()
Exemple #3
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    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()
Exemple #4
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"""
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)