Get missing bonds#

Getting the missing bonds.

A molecular system can have missing bonds. The function molsysmt.build.get_missing_bonds() can detect this lack of bonds returning the pairs of atoms that should be covalently bonded.

Added in version 1.0.0.

How this function works#

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function:molsysmt.build.get_missing_bonds().

Let’s see this function in action: We begin by converting the structure into a standard MolSysMT object.

import molsysmt as msm

#molsys = msm.convert(msm.systems['nglview']['md_1u19.pdb'],
#                     to_form='molsysmt.MolSys')

molsys = msm.build.build_peptide('AceAlaNme')

msm.get(molsys, element='bond', selection=[0,1,2], bonded_atoms=True)

[0, 1, 2, 3]

msm.info(molsys, element='atom')

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
0	1	H1	H	0	1	ACE	terminal capping	peptide	peptide 0
1	2	CH3	C	0	1	ACE	terminal capping	peptide	peptide 0
2	3	H2	H	0	1	ACE	terminal capping	peptide	peptide 0
3	4	H3	H	0	1	ACE	terminal capping	peptide	peptide 0
4	5	C	C	0	1	ACE	terminal capping	peptide	peptide 0
5	6	O	O	0	1	ACE	terminal capping	peptide	peptide 0
6	7	N	N	1	2	ALA	amino acid	peptide	peptide 0
7	8	H	H	1	2	ALA	amino acid	peptide	peptide 0
8	9	CA	C	1	2	ALA	amino acid	peptide	peptide 0
9	10	HA	H	1	2	ALA	amino acid	peptide	peptide 0
10	11	CB	C	1	2	ALA	amino acid	peptide	peptide 0
11	12	HB1	H	1	2	ALA	amino acid	peptide	peptide 0
12	13	HB2	H	1	2	ALA	amino acid	peptide	peptide 0
13	14	HB3	H	1	2	ALA	amino acid	peptide	peptide 0
14	15	C	C	1	2	ALA	amino acid	peptide	peptide 0
15	16	O	O	1	2	ALA	amino acid	peptide	peptide 0
16	17	N	N	2	3	NME	terminal capping	peptide	peptide 0
17	18	H	H	2	3	NME	terminal capping	peptide	peptide 0
18	19	C	C	2	3	NME	terminal capping	peptide	peptide 0
19	20	H1	H	2	3	NME	terminal capping	peptide	peptide 0
20	21	H2	H	2	3	NME	terminal capping	peptide	peptide 0
21	22	H3	H	2	3	NME	terminal capping	peptide	peptide 0

msm.build.remove_bonds(molsys, bond_indices=[0])

molsys.topology.groups

	group_id	group_name	group_type
0	1	ACE	terminal capping
1	2	ALA	amino acid
2	3	NME	terminal capping

msm.info(molsys, element='atom')

index	id	name	type	group index	group id	group name	group type	component index	molecule type	entity name
0	1	H1	H	0	1	ACE	terminal capping	0	peptide	peptide 0
1	2	CH3	C	0	1	ACE	terminal capping	1	peptide	peptide 0
2	3	H2	H	0	1	ACE	terminal capping	1	peptide	peptide 0
3	4	H3	H	0	1	ACE	terminal capping	1	peptide	peptide 0
4	5	C	C	0	1	ACE	terminal capping	1	peptide	peptide 0
5	6	O	O	0	1	ACE	terminal capping	1	peptide	peptide 0
6	7	N	N	1	2	ALA	amino acid	1	peptide	peptide 0
7	8	H	H	1	2	ALA	amino acid	1	peptide	peptide 0
8	9	CA	C	1	2	ALA	amino acid	1	peptide	peptide 0
9	10	HA	H	1	2	ALA	amino acid	1	peptide	peptide 0
10	11	CB	C	1	2	ALA	amino acid	1	peptide	peptide 0
11	12	HB1	H	1	2	ALA	amino acid	1	peptide	peptide 0
12	13	HB2	H	1	2	ALA	amino acid	1	peptide	peptide 0
13	14	HB3	H	1	2	ALA	amino acid	1	peptide	peptide 0
14	15	C	C	1	2	ALA	amino acid	1	peptide	peptide 0
15	16	O	O	1	2	ALA	amino acid	1	peptide	peptide 0
16	17	N	N	2	3	NME	terminal capping	1	peptide	peptide 0
17	18	H	H	2	3	NME	terminal capping	1	peptide	peptide 0
18	19	C	C	2	3	NME	terminal capping	1	peptide	peptide 0
19	20	H1	H	2	3	NME	terminal capping	1	peptide	peptide 0
20	21	H2	H	2	3	NME	terminal capping	1	peptide	peptide 0
21	22	H3	H	2	3	NME	terminal capping	1	peptide	peptide 0

msm.element.component.get_component_index(molsys, redefine_indices=True)

[0, 1]

msm.build.get_missing_bonds(molsys)

[[0, 1]]

msm.info(molsys, element='atom')

index	id	name	type	group index	group id	group name	group type	component index	molecule type	entity name
0	1	H1	H	0	1	ACE	terminal capping	0	peptide	peptide 0
1	2	CH3	C	0	1	ACE	terminal capping	1	peptide	peptide 0
2	3	H2	H	0	1	ACE	terminal capping	1	peptide	peptide 0
3	4	H3	H	0	1	ACE	terminal capping	1	peptide	peptide 0
4	5	C	C	0	1	ACE	terminal capping	1	peptide	peptide 0
5	6	O	O	0	1	ACE	terminal capping	1	peptide	peptide 0
6	7	N	N	1	2	ALA	amino acid	1	peptide	peptide 0
7	8	H	H	1	2	ALA	amino acid	1	peptide	peptide 0
8	9	CA	C	1	2	ALA	amino acid	1	peptide	peptide 0
9	10	HA	H	1	2	ALA	amino acid	1	peptide	peptide 0
10	11	CB	C	1	2	ALA	amino acid	1	peptide	peptide 0
11	12	HB1	H	1	2	ALA	amino acid	1	peptide	peptide 0
12	13	HB2	H	1	2	ALA	amino acid	1	peptide	peptide 0
13	14	HB3	H	1	2	ALA	amino acid	1	peptide	peptide 0
14	15	C	C	1	2	ALA	amino acid	1	peptide	peptide 0
15	16	O	O	1	2	ALA	amino acid	1	peptide	peptide 0
16	17	N	N	2	3	NME	terminal capping	1	peptide	peptide 0
17	18	H	H	2	3	NME	terminal capping	1	peptide	peptide 0
18	19	C	C	2	3	NME	terminal capping	1	peptide	peptide 0
19	20	H1	H	2	3	NME	terminal capping	1	peptide	peptide 0
20	21	H2	H	2	3	NME	terminal capping	1	peptide	peptide 0
21	22	H3	H	2	3	NME	terminal capping	1	peptide	peptide 0