dummy.py at fcab626 ⋅ slochower/pAPRika

import os as os

import parmed as pmd
from parmed.structure import Structure as ParmedStructureClass

from paprika import utils


def add_dummy(
    structure,
    atom_name="DUM",
    residue_name="DUM",
    mass=208.00,
    atomic_number=82,
    x=0.000,
    y=0.000,
    z=0.000,
):
    """Add a dummy atom at the specified coordinates to the end of a structure.

    Parameters
    ----------
    structure : str or :class:`parmed.Structure`
        The structure to be modified
    atom_name : str, optional, default='DUM'
        The name of the dummy atom.
    residue_name : str, optional, default='DUM'
        The residue name of the dummy atom.
    mass : float, optional, default=208.0
        The mass of the dummy atom.
    atomic_number : int, optional, default=82
        The element of the dummy atom.
    x : float, optional, default=0.0
        The x coordinate of the dummy atom.
    y : float, optional, default=0.0
        The y coordinate of the dummy atom.
    z : float, optional, default=0.0
        The z coordinate of the dummy atom.

    Returns
    -------
    structure : :class:`parmed.Structure`
        The modified structure with dummy atoms added.

    """

    if isinstance(structure, str):
        structure = utils.return_parmed_structure(structure)
    elif isinstance(structure, ParmedStructureClass):
        pass
    else:
        raise Exception(
            "add_dummy does not support the type associated with structure: "
            + type(structure)
        )

    # Create an atom object
    dum = pmd.topologyobjects.Atom()
    dum.name = atom_name
    dum.mass = mass
    dum.atomic_number = atomic_number
    # This may be a problem if these coordinates are outside the periodic box
    # dimensions and ParmEd does not recalculate the box vectors before saving
    # `inpcrd`...
    dum.xx = x
    dum.xy = y
    dum.xz = z

    # Assume that the last atom in the structure has the highest atom index,
    # so the new atom will be at the end.
    dum.number = structure.atoms[-1].number + 1
    # Assume that the last residue in the structure has the highest residue
    # number, so the new atom will be at the end.
    residue_num = structure.residues[-1].number + 1

    structure.add_atom(dum, residue_name, residue_num)

    # Make sure that atom.number get set properly.  When reading in prmtop/inpcrd
    # parmed doesn't seem to set atom.number for some reason.
    for i, atom in enumerate(structure.atoms):
        atom.number = structure.atoms[i].idx + 1

    # tleap will probably want TER cards in any PDBs we make, so enforce
    # that for both the dummy residue and the residue before it
    structure.residues[-2].ter = True
    structure.residues[-1].ter = True

    return structure


def write_dummy_frcmod(
    atom_type="Du", mass="208.00", path="./", filename="dummy.frcmod", filepath=None
):
    """Write a ``frcmod`` file for dummy atoms.

    Parameters
    ----------
    atom_type : str, optional, default='Du'
        The atom type of the dummy atom.
    mass : str, optional, default=208.00
        The mass of the dummy atom.
    path : str, optional, default='./
        The directory of the output file, if `filepath` is not specified.
    filename : str, optional, default='dummy.frcmod`
        The name of the output file, if `filepath` is not specified.
    filepath : str, optional, default=None
        The full path (directory and file) of the output.

    """

    if filepath is None:
        filepath = os.path.join(path, filename)

    with open(filepath, "w") as f:
        f.write(
            """\
Parameters for dummy atom with type {0}
MASS
{0}     {1}

BOND

ANGLE

DIHE

IMPROPER

NONBON
  {0}       0.000     0.0000000
""".format(
                atom_type, mass
            )
        )


def write_dummy_mol2(
    atom_name="DUM",
    atom_type="Du",
    residue_name="DUM",
    path="./",
    filename="dummy.mol2",
    filepath=None,
):
    """Write a ``mol2`` file for dummy atoms.

    Parameters
    ----------
    atom_name : str, optional, default='DUM'
        The atom name of the dummy atoms.
    atom_type : str, optional, default='Du'
        The atom type of the dummy atoms.
    residue_name : str, optional, default='DUM'
        The residue name of the dummy atoms.
    path : str, optional, default='./'
        The directory of the output file, if `filepath` is not specified.
    filename : str, optional, default='dummy.mol2'
        The name of the output file, if `filepath` is not specified.
    filepath : str, optional, default=None
        The full path (directory and file) of the output.

    """

    if filepath is None:
        filepath = os.path.join(path, filename)

    with open(filepath, "w") as f:
        f.write(
            """\
@<TRIPOS>MOLECULE
{0}
    1     0     1     0     1
SMALL
USER_CHARGES

@<TRIPOS>ATOM
  1 {1:4s}    0.000000    0.000000    0.000000 {2}    1 {0}     0.0000 ****
@<TRIPOS>BOND
@<TRIPOS>SUBSTRUCTURE
      1  {0}              1 ****               0 ****  ****    0 ROOT
""".format(
                residue_name[0:3], atom_name, atom_type[0:2]
            )
        )


def extract_dummy_atoms(structure, resname=None, serial=True):
    """
    Extract information about dummy atoms from a parmed structure and
    returns the information as a dictionary.

    Parameters
    ----------
    structure : :class:`parmed.Structure`
        The parmed structure object we want to extract from
    resname : list
        List of residue name for the dummy atoms (default: ["DM1", "DM2", "DM3"])
    serial : bool
        get indices in serial (starts from 1) or index (starts from 0)

    Returns
    -------
    dummy_atoms : dict
        A dictionary containing positions (``pos``), index (``idx``) and mass (``mass``) of dummy atoms.
    """

    if resname is None:
        resname = ["DM1", "DM2", "DM3"]

    dummy_atoms = {name: {} for name in resname}

    for dummy_atom in resname:
        residue = f":{dummy_atom}"
        dummy_atoms[dummy_atom]["pos"] = structure[residue].coordinates[0]
        dummy_atoms[dummy_atom]["mass"] = [
            atom.mass for atom in structure[residue].atoms
        ][0]
        dummy_atoms[dummy_atom]["idx"] = utils.index_from_mask(
            structure, residue, amber_index=serial
        )[0]
        dummy_atoms[dummy_atom]["idx_type"] = "serial" if serial else "index"

    return dummy_atoms

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1	38	import os as os
2
3	38	import parmed as pmd
4	38	from parmed.structure import Structure as ParmedStructureClass
5
6	38	from paprika import utils
7
8
9	38	def add_dummy(
10		structure,
11		atom_name="DUM",
12		residue_name="DUM",
13		mass=208.00,
14		atomic_number=82,
15		x=0.000,
16		y=0.000,
17		z=0.000,
18		):
19		"""Add a dummy atom at the specified coordinates to the end of a structure.
20
21		Parameters
22		----------
23		structure : str or :class:`parmed.Structure`
24		The structure to be modified
25		atom_name : str, optional, default='DUM'
26		The name of the dummy atom.
27		residue_name : str, optional, default='DUM'
28		The residue name of the dummy atom.
29		mass : float, optional, default=208.0
30		The mass of the dummy atom.
31		atomic_number : int, optional, default=82
32		The element of the dummy atom.
33		x : float, optional, default=0.0
34		The x coordinate of the dummy atom.
35		y : float, optional, default=0.0
36		The y coordinate of the dummy atom.
37		z : float, optional, default=0.0
38		The z coordinate of the dummy atom.
39
40		Returns
41		-------
42		structure : :class:`parmed.Structure`
43		The modified structure with dummy atoms added.
44
45		"""
46
47	38	if isinstance(structure, str):
48	0	structure = utils.return_parmed_structure(structure)
49	38	elif isinstance(structure, ParmedStructureClass):
50	38	pass
51		else:
52	0	raise Exception(
53		"add_dummy does not support the type associated with structure: "
54		+ type(structure)
55		)
56
57		# Create an atom object
58	38	dum = pmd.topologyobjects.Atom()
59	38	dum.name = atom_name
60	38	dum.mass = mass
61	38	dum.atomic_number = atomic_number
62		# This may be a problem if these coordinates are outside the periodic box
63		# dimensions and ParmEd does not recalculate the box vectors before saving
64		# `inpcrd`...
65	38	dum.xx = x
66	38	dum.xy = y
67	38	dum.xz = z
68
69		# Assume that the last atom in the structure has the highest atom index,
70		# so the new atom will be at the end.
71	38	dum.number = structure.atoms[-1].number + 1
72		# Assume that the last residue in the structure has the highest residue
73		# number, so the new atom will be at the end.
74	38	residue_num = structure.residues[-1].number + 1
75
76	38	structure.add_atom(dum, residue_name, residue_num)
77
78		# Make sure that atom.number get set properly. When reading in prmtop/inpcrd
79		# parmed doesn't seem to set atom.number for some reason.
80	38	for i, atom in enumerate(structure.atoms):
81	38	atom.number = structure.atoms[i].idx + 1
82
83		# tleap will probably want TER cards in any PDBs we make, so enforce
84		# that for both the dummy residue and the residue before it
85	38	structure.residues[-2].ter = True
86	38	structure.residues[-1].ter = True
87
88	38	return structure
89
90
91	38	def write_dummy_frcmod(
92		atom_type="Du", mass="208.00", path="./", filename="dummy.frcmod", filepath=None
93		):
94		"""Write a ``frcmod`` file for dummy atoms.
95
96		Parameters
97		----------
98		atom_type : str, optional, default='Du'
99		The atom type of the dummy atom.
100		mass : str, optional, default=208.00
101		The mass of the dummy atom.
102		path : str, optional, default='./
103		The directory of the output file, if `filepath` is not specified.
104		filename : str, optional, default='dummy.frcmod`
105		The name of the output file, if `filepath` is not specified.
106		filepath : str, optional, default=None
107		The full path (directory and file) of the output.
108
109		"""
110
111	38	if filepath is None:
112	38	filepath = os.path.join(path, filename)
113
114	38	with open(filepath, "w") as f:
115	38	f.write(
116		"""\
117		Parameters for dummy atom with type {0}
118		MASS
119		{0} {1}
120
121		BOND
122
123		ANGLE
124
125		DIHE
126
127		IMPROPER
128
129		NONBON
130		{0} 0.000 0.0000000
131		""".format(
132		atom_type, mass
133		)
134		)
135
136
137	38	def write_dummy_mol2(
138		atom_name="DUM",
139		atom_type="Du",
140		residue_name="DUM",
141		path="./",
142		filename="dummy.mol2",
143		filepath=None,
144		):
145		"""Write a ``mol2`` file for dummy atoms.
146
147		Parameters
148		----------
149		atom_name : str, optional, default='DUM'
150		The atom name of the dummy atoms.
151		atom_type : str, optional, default='Du'
152		The atom type of the dummy atoms.
153		residue_name : str, optional, default='DUM'
154		The residue name of the dummy atoms.
155		path : str, optional, default='./'
156		The directory of the output file, if `filepath` is not specified.
157		filename : str, optional, default='dummy.mol2'
158		The name of the output file, if `filepath` is not specified.
159		filepath : str, optional, default=None
160		The full path (directory and file) of the output.
161
162		"""
163
164	38	if filepath is None:
165	38	filepath = os.path.join(path, filename)
166
167	38	with open(filepath, "w") as f:
168	38	f.write(
169		"""\
170		@<TRIPOS>MOLECULE
171		{0}
172		1 0 1 0 1
173		SMALL
174		USER_CHARGES
175
176		@<TRIPOS>ATOM
177		1 {1:4s} 0.000000 0.000000 0.000000 {2} 1 {0} 0.0000 ****
178		@<TRIPOS>BOND
179		@<TRIPOS>SUBSTRUCTURE
180		1 {0} 1 ** 0 ** 0 ROOT
181		""".format(
182		residue_name[0:3], atom_name, atom_type[0:2]
183		)
184		)
185
186
187	38	def extract_dummy_atoms(structure, resname=None, serial=True):
188		"""
189		Extract information about dummy atoms from a parmed structure and
190		returns the information as a dictionary.
191
192		Parameters
193		----------
194		structure : :class:`parmed.Structure`
195		The parmed structure object we want to extract from
196		resname : list
197		List of residue name for the dummy atoms (default: ["DM1", "DM2", "DM3"])
198		serial : bool
199		get indices in serial (starts from 1) or index (starts from 0)
200
201		Returns
202		-------
203		dummy_atoms : dict
204		A dictionary containing positions (``pos``), index (``idx``) and mass (``mass``) of dummy atoms.
205		"""
206
207	38	if resname is None:
208	38	resname = ["DM1", "DM2", "DM3"]
209
210	38	dummy_atoms = {name: {} for name in resname}
211
212	38	for dummy_atom in resname:
213	38	residue = f":{dummy_atom}"
214	38	dummy_atoms[dummy_atom]["pos"] = structure[residue].coordinates[0]
215	38	dummy_atoms[dummy_atom]["mass"] = [
216		atom.mass for atom in structure[residue].atoms
217		][0]
218	38	dummy_atoms[dummy_atom]["idx"] = utils.index_from_mask(
219		structure, residue, amber_index=serial
220		)[0]
221	38	dummy_atoms[dummy_atom]["idx_type"] = "serial" if serial else "index"
222
223	38	return dummy_atoms