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In process of adding bonds
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@dprada
dprada committed Mar 17, 2024
1 parent dd23817 commit 9eb9e06
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Showing 8 changed files with 115 additions and 43 deletions.
1 change: 1 addition & 0 deletions molsysmt/build/__init__.py
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@@ -1,3 +1,4 @@
from .add_bonds import add_bonds
from .add_missing_hydrogens import add_missing_hydrogens
from .add_missing_heavy_atoms import add_missing_heavy_atoms
from .add_missing_terminal_cappings import add_missing_terminal_cappings
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22 changes: 22 additions & 0 deletions molsysmt/build/add_bonds.py
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@@ -0,0 +1,22 @@
from molsysmt._private.exceptions import NotImplementedMethodError
from molsysmt._private.digestion import digest
from molsysmt._private.variables import is_all

@digest()
def add_bonds(molecular_system, bonded_atom_pairs, in_place=True, skip_digestion=False):

from molsysmt.basic import where_is_attribute
from molsysmt.form import _dict_modules

if in_place:

item, form = where_is_attribute(molecular_system, 'bonded_atom_pairs', check_if_None=False,
skip_digestion=True)

add_bonds_function = getattr(_dict_modules[form], f'add_bonds')
add_bonds_function(item, bonded_atom_pairs)

else:

raise NotImplementedMethodError

29 changes: 17 additions & 12 deletions molsysmt/build/add_missing_bonds.py
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@@ -1,23 +1,28 @@
from molsysmt._private.exceptions import *
from molsysmt._private.digestion import *

def add_missing_bonds(molecular_system, threshold='2 angstroms', engine='MolSysMT', check=True):
from molsysmt._private.exceptions import NotImplementedMethodError
from molsysmt._private.digestion import digest
from molsysmt._private.variables import is_all

@digest()
def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all',
structure_indices=0, syntax='MolSysMT', engine='MolSysMT',
with_templates=True, with_distances=True, skip_digestion=False):
"""
To be written soon...
"""

if check:
if engine=='MolSysMT':

digest_single_molecular_system(molecular_system)
engine = digest_engine(engine)
from molsysmt.build import get_missing_bonds
from molsysmt.build import add_bonds

from molsysmt.basic import convert, get_form
bonds = get_missing_bonds(molecular_system, threshold=threshold, selection=selection,
structure_indices=structure_indices, syntax=syntax,
with_templates=with_templates, with_distances=with_distances,
skip_digestion=True)

output_molecular_system = None
form_in = get_form(molecular_system)
form_out = form_in
add_bonds(molecular_system, bonds, in_place=True)

if engine=="ParmEd":
elif engine=="ParmEd":

raise NotImplementedError

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1 change: 1 addition & 0 deletions molsysmt/form/molsysmt_MolSys/__init__.py
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Expand Up @@ -11,6 +11,7 @@
from .copy import copy
from .add import add
from .merge import merge
from .add_bonds import add_bonds
from .append_structures import append_structures
from .get_topological_attributes import *
from .get_structural_attributes import *
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10 changes: 10 additions & 0 deletions molsysmt/form/molsysmt_MolSys/add_bonds.py
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@@ -0,0 +1,10 @@
from molsysmt._private.exceptions import NotImplementedMethodError
from molsysmt._private.digestion import digest
from molsysmt import pyunitwizard as puw
import numpy as np

@digest(form='molsysmt.MolSys')
def add_bonds(item, bonded_atom_pairs, skip_digestion=False):

item.topology.add_bonds(bonded_atom_pairs, skip_digestion=True)

4 changes: 2 additions & 2 deletions molsysmt/form/molsysmt_MolSys/add.py → ...t/form/molsysmt_MolSys/add_from_system.py
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Expand Up @@ -3,8 +3,8 @@
from molsysmt import pyunitwizard as puw
import numpy as np

@digest(form='molsysmt.MolSys', to_form='molsysmt.MolSys')
def add(to_item, item, atom_indices='all', structure_indices='all', skip_digestion=False):
@digest(to_form='molsysmt.MolSys', from_form='molsysmt.MolSys')
def add(to_item, from_item, atom_indices='all', structure_indices='all', skip_digestion=False):

to_item.add(item, atom_indices=atom_indices, structure_indices=structure_indices, skip_digestion=True)

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12 changes: 12 additions & 0 deletions molsysmt/native/topology.py
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Expand Up @@ -307,6 +307,18 @@ def copy(self):

return tmp_item

def add_bonds(self, bonded_atom_pairs, skip_digestion=False):

bonded_atom_pairs = np.array(bonded_atom_pairs)
n_bonds = bonded_atom_pairs.shape[0]

aux_bonds_dataframe = Bonds_DataFrame(n_bonds=n_bonds)
aux_bonds_dataframe.atom1_index=bonded_atom_pairs[:,0]
aux_bonds_dataframe.atom2_index=bonded_atom_pairs[:,1]


df_concatenado = pd.concat([df_original, nuevas_filas], ignore_index=True)

def add_missing_bonds(self, selection='all', syntax='MolSysMT', skip_digestion=False):

from molsysmt.build import get_missing_bonds as _get_missing_bonds
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79 changes: 50 additions & 29 deletions sandbox/Test_2nzt.ipynb
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Expand Up @@ -28,7 +28,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "43d00da87d8f4eb9ab66f260776766db",
"model_id": "aa9738c1f95c4ac1a9b2860e80c5dc29",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -44,7 +44,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"id": "a521ba75-1a05-4d64-b906-448f38e27101",
"metadata": {},
"outputs": [],
Expand All @@ -54,42 +54,63 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 7,
"id": "675072b0-c2db-4296-9363-7b287c564b03",
"metadata": {},
"outputs": [
{
"ename": "AttributeError",
"evalue": "'str' object has no attribute 'entry'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[5], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m molsys \u001b[38;5;241m=\u001b[39m \u001b[43mmsm\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconvert\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:122\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 120\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m func(all_args[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m], \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mfinal_args)\n\u001b[1;32m 121\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 122\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mfinal_args\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/convert.py:530\u001b[0m, in \u001b[0;36mconvert\u001b[0;34m(molecular_system, to_form, selection, structure_indices, syntax, verbose, skip_digestion, **kwargs)\u001b[0m\n\u001b[1;32m 527\u001b[0m \u001b[38;5;66;03m# If one to one\u001b[39;00m\n\u001b[1;32m 528\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(from_form, (\u001b[38;5;28mlist\u001b[39m, \u001b[38;5;28mtuple\u001b[39m)):\n\u001b[0;32m--> 530\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43m_convert_one_to_one\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfrom_form\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mto_form\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mto_form\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mselection\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mselection\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 531\u001b[0m \u001b[43m \u001b[49m\u001b[43msyntax\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msyntax\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mverbose\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 533\u001b[0m \u001b[38;5;66;03m# If multiple to one\u001b[39;00m\n\u001b[1;32m 534\u001b[0m \n\u001b[1;32m 535\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 536\u001b[0m \n\u001b[1;32m 537\u001b[0m \u001b[38;5;66;03m# conversions in private shortcuts\u001b[39;00m\n\u001b[1;32m 538\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mtuple\u001b[39m(\u001b[38;5;28msorted\u001b[39m(from_form)) \u001b[38;5;129;01min\u001b[39;00m _multiple_conversion_shortcuts:\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/basic/convert.py:84\u001b[0m, in \u001b[0;36m_convert_one_to_one\u001b[0;34m(molecular_system, from_form, to_form, selection, structure_indices, syntax, verbose, **kwargs)\u001b[0m\n\u001b[1;32m 81\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(missing_arguments)\u001b[38;5;241m>\u001b[39m\u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 82\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m NotCompatibleConversionError(from_form, to_form, missing_arguments)\n\u001b[0;32m---> 84\u001b[0m output \u001b[38;5;241m=\u001b[39m \u001b[43mfunction\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmolecular_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mconversion_arguments\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m _dict_modules[from_form]\u001b[38;5;241m.\u001b[39m_convert_to) \u001b[38;5;129;01mand\u001b[39;00m (to_form \u001b[38;5;129;01min\u001b[39;00m _dict_modules[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m.\u001b[39m_convert_to):\n\u001b[1;32m 88\u001b[0m output \u001b[38;5;241m=\u001b[39m _convert_one_to_one(molecular_system, from_form, to_form\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolsysmt.MolSys\u001b[39m\u001b[38;5;124m'\u001b[39m, selection\u001b[38;5;241m=\u001b[39mselection,\n\u001b[1;32m 89\u001b[0m structure_indices\u001b[38;5;241m=\u001b[39mstructure_indices, syntax\u001b[38;5;241m=\u001b[39msyntax, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 54\u001b[0m \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m 56\u001b[0m caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/file_pdb/to_molsysmt_MolSys.py:11\u001b[0m, in \u001b[0;36mto_molsysmt_MolSys\u001b[0;34m(item, atom_indices, structure_indices, get_missing_bonds, skip_digestion)\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmolsysmt_PDBFileHandler\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m to_molsysmt_MolSys \u001b[38;5;28;01mas\u001b[39;00m molsysmt_PDBFileHandler_to_molsysmt_MolSys\n\u001b[1;32m 10\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m to_molsysmt_PDBFileHandler(item, skip_digestion\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[0;32m---> 11\u001b[0m tmp_item \u001b[38;5;241m=\u001b[39m \u001b[43mmolsysmt_PDBFileHandler_to_molsysmt_MolSys\u001b[49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43matom_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43matom_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 12\u001b[0m \u001b[43m \u001b[49m\u001b[43mstructure_indices\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mstructure_indices\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[43m \u001b[49m\u001b[43mget_missing_bonds\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mget_missing_bonds\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 14\u001b[0m \u001b[43m \u001b[49m\u001b[43mskip_digestion\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m tmp_item\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/_private/digestion/digest.py:52\u001b[0m, in \u001b[0;36mdigest.<locals>.digestor.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[38;5;129m@functools\u001b[39m\u001b[38;5;241m.\u001b[39mwraps(func)\n\u001b[1;32m 49\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mwrapper\u001b[39m(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 51\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m kwargs\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mskip_digestion\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m---> 52\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 54\u001b[0m \u001b[38;5;66;03m# Define caller\u001b[39;00m\n\u001b[1;32m 56\u001b[0m caller \u001b[38;5;241m=\u001b[39m func\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__module__\u001b[39m\u001b[38;5;241m+\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;241m+\u001b[39mfunc\u001b[38;5;241m.\u001b[39m\u001b[38;5;18m__name__\u001b[39m\n",
"File \u001b[0;32m~/repos@uibcdf/MolSysMT/molsysmt/form/molsysmt_PDBFileHandler/to_molsysmt_MolSys.py:34\u001b[0m, in \u001b[0;36mto_molsysmt_MolSys\u001b[0;34m(item, atom_indices, structure_indices, get_missing_bonds, skip_digestion)\u001b[0m\n\u001b[1;32m 31\u001b[0m former_chain_name \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 32\u001b[0m aux_dict_chain \u001b[38;5;241m=\u001b[39m {}\n\u001b[0;32m---> 34\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m atom_record \u001b[38;5;129;01min\u001b[39;00m \u001b[43mitem\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mentry\u001b[49m\u001b[38;5;241m.\u001b[39mcoordinate\u001b[38;5;241m.\u001b[39mmodel[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mrecord:\n\u001b[1;32m 36\u001b[0m atom_id_array\u001b[38;5;241m.\u001b[39mappend(atom_record\u001b[38;5;241m.\u001b[39mserial)\n\u001b[1;32m 37\u001b[0m atom_name_array\u001b[38;5;241m.\u001b[39mappend(atom_record\u001b[38;5;241m.\u001b[39mname)\n",
"\u001b[0;31mAttributeError\u001b[0m: 'str' object has no attribute 'entry'"
]
}
],
"outputs": [],
"source": [
"molsys = msm.convert(file)"
"molsys = msm.convert(file, get_missing_bonds=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "74caa585-af95-44c6-a674-7f53d577b7e3",
"execution_count": 6,
"id": "8d511c53-0ae3-49e1-a9cc-b4b76c6907ce",
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/html": [
"<style type=\"text/css\">\n",
"</style>\n",
"<table id=\"T_b755e\">\n",
" <thead>\n",
" <tr>\n",
" <th id=\"T_b755e_level0_col0\" class=\"col_heading level0 col0\" >form</th>\n",
" <th id=\"T_b755e_level0_col1\" class=\"col_heading level0 col1\" >n_atoms</th>\n",
" <th id=\"T_b755e_level0_col2\" class=\"col_heading level0 col2\" >n_groups</th>\n",
" <th id=\"T_b755e_level0_col3\" class=\"col_heading level0 col3\" >n_components</th>\n",
" <th id=\"T_b755e_level0_col4\" class=\"col_heading level0 col4\" >n_chains</th>\n",
" <th id=\"T_b755e_level0_col5\" class=\"col_heading level0 col5\" >n_molecules</th>\n",
" <th id=\"T_b755e_level0_col6\" class=\"col_heading level0 col6\" >n_entities</th>\n",
" <th id=\"T_b755e_level0_col7\" class=\"col_heading level0 col7\" >n_structures</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <td id=\"T_b755e_row0_col0\" class=\"data row0 col0\" >molsysmt.MolSys</td>\n",
" <td id=\"T_b755e_row0_col1\" class=\"data row0 col1\" >7158</td>\n",
" <td id=\"T_b755e_row0_col2\" class=\"data row0 col2\" >917</td>\n",
" <td id=\"T_b755e_row0_col3\" class=\"data row0 col3\" >0</td>\n",
" <td id=\"T_b755e_row0_col4\" class=\"data row0 col4\" >1</td>\n",
" <td id=\"T_b755e_row0_col5\" class=\"data row0 col5\" >0</td>\n",
" <td id=\"T_b755e_row0_col6\" class=\"data row0 col6\" >0</td>\n",
" <td id=\"T_b755e_row0_col7\" class=\"data row0 col7\" >1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n"
],
"text/plain": [
"<pandas.io.formats.style.Styler at 0x7fa26bcdc160>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"%%time\n",
"molsys = msm.convert(handler, 'molsysmt.MolSys', get_missing_bonds=True)"
"msm.info(molsys)"
]
},
{
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