Get donor atoms#

import molsysmt as msm

msm.hbonds.donor_inclusion_rules

["(atom_type=='O') bonded to (atom_type=='H')",
 "(atom_type=='N') bonded to (atom_type=='H')"]

 msm.hbonds.donor_exclusion_rules

["(atom_name=='NE2') not bonded to (atom_type=='H')",
 "(atom_name=='ND1') not bonded to (atom_type=='H')"]

molsys = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35.h5msm'])

donor_atoms = msm.hbonds.get_donor_atoms(molsys, selection="group_index==[1,2,3]")

donor_atoms

array([[ 6,  7],
       [23, 24],
       [42, 43],
       [51, 52]])

msm.info(molsys, element='atom', selection=donor_atoms[:,0])

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
6	7	N	N	1	41	MET	amino acid	peptide	VILLIN
23	24	N	N	2	42	LEU	amino acid	peptide	VILLIN
42	43	N	N	3	43	SER	amino acid	peptide	VILLIN
51	52	OG	O	3	43	SER	amino acid	peptide	VILLIN

msm.info(molsys, element='atom', selection=donor_atoms[:,1])

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
7	8	H	H	1	41	MET	amino acid	peptide	VILLIN
24	25	H	H	2	42	LEU	amino acid	peptide	VILLIN
43	44	H	H	3	43	SER	amino acid	peptide	VILLIN
52	53	HG	H	3	43	SER	amino acid	peptide	VILLIN

msm.info(molsys, element='atom', selection=donor_atoms[0])

index	id	name	type	group index	group id	group name	group type	component index	chain index	molecule index	molecule type	entity index	entity name
6	7	N	N	1	41	MET	amino acid	0	0	0	peptide	0	VILLIN
7	8	H	H	1	41	MET	amino acid	0	0	0	peptide	0	VILLIN

donor_atoms = msm.hbonds.get_donor_atoms(molsys, selection="group_index==[1,2,3]",
                                         inclusion_rules="atom_name=='CB'", exclusion_rules="group_name=='SER'",
                                         default_inclusion_rules=False, default_exclusion_rules=False)

donor_atoms

array([[12, 13],
       [12, 14],
       [29, 30],
       [29, 31]])

msm.info(molsys, element='atom', selection=donor_atoms[0])

index	id	name	type	group index	group id	group name	group type	component index	chain index	molecule index	molecule type	entity index	entity name
12	13	CB	C	1	41	MET	amino acid	0	0	0	peptide	0	VILLIN
13	14	HB2	H	1	41	MET	amino acid	0	0	0	peptide	0	VILLIN

donor_atoms = msm.hbonds.get_donor_atoms(molsys, selection="group_index==[1,2,3]",
                                         inclusion_rules="atom_name=='CB'", exclusion_rules="group_name=='SER'")

msm.info(molsys, element='atom', selection=donor_atoms[:,0])

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
6	7	N	N	1	41	MET	amino acid	peptide	VILLIN
12	13	CB	C	1	41	MET	amino acid	peptide	VILLIN
12	13	CB	C	1	41	MET	amino acid	peptide	VILLIN
23	24	N	N	2	42	LEU	amino acid	peptide	VILLIN
29	30	CB	C	2	42	LEU	amino acid	peptide	VILLIN
29	30	CB	C	2	42	LEU	amino acid	peptide	VILLIN

msm.hbonds.donor_inclusion_rules.append("atom_name=='CB'")

msm.hbonds.donor_inclusion_rules

["(atom_type=='O') bonded to (atom_type=='H')",
 "(atom_type=='N') bonded to (atom_type=='H')",
 "atom_name=='CB'"]

donor_atoms = msm.hbonds.get_donor_atoms(molsys, selection="group_index==[1,2,3]")

msm.info(molsys, element='atom', selection=donor_atoms[:,0])

index	id	name	type	group index	group id	group name	group type	molecule type	entity name
6	7	N	N	1	41	MET	amino acid	peptide	VILLIN
12	13	CB	C	1	41	MET	amino acid	peptide	VILLIN
12	13	CB	C	1	41	MET	amino acid	peptide	VILLIN
23	24	N	N	2	42	LEU	amino acid	peptide	VILLIN
29	30	CB	C	2	42	LEU	amino acid	peptide	VILLIN
29	30	CB	C	2	42	LEU	amino acid	peptide	VILLIN
42	43	N	N	3	43	SER	amino acid	peptide	VILLIN
48	49	CB	C	3	43	SER	amino acid	peptide	VILLIN
48	49	CB	C	3	43	SER	amino acid	peptide	VILLIN
51	52	OG	O	3	43	SER	amino acid	peptide	VILLIN