src.molecule.Molecule Class Reference

Lee-Ping's general file format conversion class. More...

Inheritance diagram for src.molecule.Molecule:

Collaboration diagram for src.molecule.Molecule:

Public Member Functions
def	__init__ (self, fnm=None, ftype=None, top=None, ttype=None, kwargs)
	Create a Molecule object. More...
def	__len__ (self)
	Return the number of frames in the trajectory. More...
def	__getattr__ (self, key)
	Whenever we try to get a class attribute, it first tries to get the attribute from the Data dictionary. More...
def	__setattr__ (self, key, value)
	Whenever we try to get a class attribute, it first tries to get the attribute from the Data dictionary. More...
def	__deepcopy__ (self, memo)
	Custom deepcopy method because Python 3.6 appears to have changed its behavior. More...
def	__getitem__ (self, key)
	The Molecule class has list-like behavior, so we can get slices of it. More...
def	__delitem__ (self, key)
	Similarly, in order to delete a frame, we simply perform item deletion on framewise variables. More...
def	__iter__ (self)
	List-like behavior for looping over trajectories. More...
def	__add__ (self, other)
	Add method for Molecule objects. More...
def	__iadd__ (self, other)
	Add method for Molecule objects. More...
def	repair (self, key, klast)
	Attempt to repair trivial issues that would otherwise break the object. More...
def	reorder_according_to (self, other)
	Reorder atoms according to some other Molecule object. More...
def	reorder_indices (self, other)
	Return the indices that would reorder atoms according to some other Molecule object. More...
def	append (self, other)
def	require (self, args)
def	write (self, fnm=None, ftype=None, append=False, selection=None, kwargs)
def	center_of_mass (self)
def	radius_of_gyration (self)
def	rigid_water (self)
	If one atom is oxygen and the next two are hydrogen, make the water molecule rigid. More...
def	load_frames (self, fnm, ftype=None, kwargs)
def	edit_qcrems (self, in_dict, subcalc=None)
	Edit Q-Chem rem variables with a dictionary. More...
def	add_quantum (self, other)
def	add_virtual_site (self, idx, kwargs)
	Add a virtual site to the system. More...
def	replace_peratom (self, key, orig, want)
	Replace all of the data for a certain attribute in the system from orig to want. More...
def	replace_peratom_conditional (self, key1, cond, key2, orig, want)
	Replace all of the data for a attribute key2 from orig to want, contingent on key1 being equal to cond. More...
def	atom_select (self, atomslice, build_topology=True)
	Return a copy of the object with certain atoms selected. More...
def	atom_stack (self, other)
	Return a copy of the object with another molecule object appended. More...
def	align_by_moments (self)
	Align molecules using the moment of inertia. More...
def	get_populations (self)
	Return a cloned molecule object but with X-coordinates set to Mulliken charges and Y-coordinates set to Mulliken spins. More...
def	load_popxyz (self, fnm)
	Given a charge-spin xyz file, load the charges (x-coordinate) and spins (y-coordinate) into internal arrays. More...
def	align (self, smooth=False, center=True, center_mass=False, atom_select=None)
	Align molecules. More...
def	center (self, center_mass=False)
	Move geometric center to the origin. More...
def	build_bonds (self)
	Build the bond connectivity graph. More...
def	build_topology (self, force_bonds=True, kwargs)
	Create self.topology and self.molecules; these are graph representations of the individual molecules (fragments) contained in the Molecule object. More...
def	distance_matrix (self, pbc=True)
	Obtain distance matrix between all pairs of atoms. More...
def	distance_displacement (self)
	Obtain distance matrix and displacement vectors between all pairs of atoms. More...
def	rotate_bond (self, frame, aj, ak, increment=15)
	Return a new Molecule object containing the selected frame plus a number of frames where the selected dihedral angle is rotated in steps of 'increment' given in degrees. More...
def	find_clashes (self, thre=0.0, pbc=True, groups=None)
	Obtain a list of atoms that 'clash' (i.e. More...
def	rotate_check_clash (self, frame, rotate_index, thresh_hyd=1.4, thresh_hvy=1.8, printLevel=1)
	Return a new Molecule object containing the selected frame plus a number of frames where the selected dihedral angle is rotated in steps of 'increment' given in degrees. More...
def	find_angles (self)
	Return a list of 3-tuples corresponding to all of the angles in the system. More...
def	find_dihedrals (self)
	Return a list of 4-tuples corresponding to all of the dihedral angles in the system. More...
def	measure_distances (self, i, j)
def	measure_angles (self, i, j, k)
def	measure_dihedrals (self, i, j, k, l)
	Return a series of dihedral angles, given four atom indices numbered from zero. More...
def	find_rings (self, max_size=6)
	Return a list of rings in the molecule. More...
def	order_by_connectivity (self, m, i, currList, max_min_path)
	Recursive function that orders atoms based on connectivity. More...
def	aliphatic_hydrogens (self)
def	all_pairwise_rmsd (self)
	Find pairwise RMSD (super slow, not like the one in MSMBuilder.) More...
def	pathwise_rmsd (self, align=True)
	Find RMSD between frames along path. More...
def	ref_rmsd (self, i, align=True)
	Find RMSD to a reference frame. More...
def	align_center (self)
def	openmm_positions (self)
	Returns the Cartesian coordinates in the Molecule object in a list of OpenMM-compatible positions, so it is possible to type simulation.context.setPositions(Mol.openmm_positions()[0]) or something like that. More...
def	openmm_boxes (self)
	Returns the periodic box vectors in the Molecule object in a list of OpenMM-compatible boxes, so it is possible to type simulation.context.setPeriodicBoxVectors(Mol.openmm_boxes()[0]) or something like that. More...
def	split (self, fnm=None, ftype=None, method="chunks", num=None)
	Split the molecule object into a number of separate files (chunks), either by specifying the number of frames per chunk or the number of chunks. More...
def	without (self, args)
	Return a copy of the Molecule object but with certain fields deleted if they exist. More...
def	read_comm_charge_mult (self, verbose=False)
	Set charge and multiplicity from reading the comment line, formatted in a specific way. More...
def	read_qcschema (self, schema, kwargs)
def	read_xyz (self, fnm, kwargs)
	.xyz files can be TINKER formatted which is why we have the try/except here. More...
def	read_xyz0 (self, fnm, kwargs)
	Parse a .xyz file which contains several xyz coordinates, and return their elements. More...
def	read_mdcrd (self, fnm, kwargs)
	Parse an AMBER .mdcrd file. More...
def	read_inpcrd (self, fnm, kwargs)
	Parse an AMBER .inpcrd or .rst file. More...
def	read_qdata (self, fnm, kwargs)
def	read_mol2 (self, fnm, kwargs)
def	read_dcd (self, fnm, kwargs)
def	read_com (self, fnm, kwargs)
	Parse a Gaussian .com file and return a SINGLE-ELEMENT list of xyz coordinates (no multiple file support) More...
def	read_arc (self, fnm, kwargs)
	Read a TINKER .arc file. More...
def	read_gro (self, fnm, kwargs)
	Read a GROMACS .gro file. More...
def	read_charmm (self, fnm, kwargs)
	Read a CHARMM .cor (or .crd) file. More...
def	read_qcin (self, fnm, kwargs)
	Read a Q-Chem input file. More...
def	read_pdb (self, fnm, kwargs)
	Loads a PDB and returns a dictionary containing its data. More...
def	read_qcesp (self, fnm, kwargs)
def	read_qcout (self, fnm, errok=None, kwargs)
	Q-Chem output file reader, adapted for our parser. More...
def	write_qcin (self, selection, kwargs)
def	write_xyz (self, selection, kwargs)
def	get_reaxff_atom_types (self)
	Return a list of element names which maps the LAMMPS atom types to the ReaxFF elements. More...
def	write_lammps_data (self, selection, kwargs)
	Write the first frame of the selection to a LAMMPS data file for the purpose of automatically initializing a LAMMPS simulation. More...
def	write_molproq (self, selection, kwargs)
def	write_mdcrd (self, selection, kwargs)
def	write_inpcrd (self, selection, sn=None, kwargs)
def	write_arc (self, selection, kwargs)
def	write_gro (self, selection, kwargs)
def	write_dcd (self, selection, kwargs)
def	write_pdb (self, selection, kwargs)
def	write_qdata (self, selection, kwargs)
	Text quantum data format. More...
def	require_resid (self)
def	require_resname (self)
def	require_boxes (self)

Public Attributes
	Read_Tab
	The table of file readers. More...
	Write_Tab
	The table of file writers. More...
	Funnel
	A funnel dictionary that takes redundant file types and maps them down to a few. More...
	positive_resid
	Creates entries like 'gromacs' : 'gromacs' and 'xyz' : 'xyz' in the Funnel. More...
	built_bonds
	top_settings
	Topology settings. More...
	Data
	comms
	Read in stuff if we passed in a file name, otherwise return an empty instance. More...
	fout
	I needed to add in this line because the DCD writer requires the file name, but the other methods don't. More...
	qm_mulliken_charges
	qm_mulliken_spins
	topology
	molecules
	charge
	mult
	xyzs
	atomname
	resid
	resname
	boxes

Detailed Description

Lee-Ping's general file format conversion class.

The purpose of this class is to read and write chemical file formats in a way that is convenient for research. There are highly general file format converters out there (e.g. catdcd, openbabel) but I find that writing my own class can be very helpful for specific purposes. Here are some things this class can do:

• Convert a .gro file to a .xyz file, or a .pdb file to a .dcd file. Data is stored internally, so any readable file can be converted into any writable file as long as there is sufficient information to write that file.
• Accumulate information from different files. For example, we may read A.gro to get a list of coordinates, add quantum settings from a B.in file, and write A.in (this gives us a file that we can use to run QM calculations)
• Concatenate two trajectories together as long as they're compatible. This is done by creating two Molecule objects and then simply adding them. Addition means two things: (1) Information fields missing from each class, but present in the other, are added to the sum, and (2) Appendable or per-frame fields (i.e. coordinates) are concatenated together.
• Slice trajectories using reasonable Python language. That is to say, MyMolecule[1:10] returns a new Molecule object that contains frames 1 through 9 (inclusive and numbered starting from zero.)

Special variables: These variables cannot be set manually because there is a special method associated with getting them.

na = The number of atoms. You'll get this if you use MyMol.na or MyMol['na']. ns = The number of snapshots. You'll get this if you use MyMol.ns or MyMol['ns'].

Unit system: Angstroms.

Definition at line 1182 of file molecule.py.

Constructor & Destructor Documentation

__init__()

def src.molecule.Molecule.__init__	(		self,
			fnm = None,
			ftype = None,
			top = None,
			ttype = None,
			kwargs
	)

Create a Molecule object.

Parameters

fnm : str, optional File name to create the Molecule object from. If provided, the file will be parsed and used to fill in the fields such as elem (elements), xyzs (coordinates) and so on. If ftype is not provided, will automatically try to determine file type from file extension. If not provided, will create an empty object. ftype : str, optional File type, corresponding to an entry in the internal table of known file types. Provide this if you have a nonstandard file extension or if you wish to force to invoke a particular parser. top : str, optional "Topology" file name. If provided, will build the Molecule using this file name, then "fnm" will load frames instead. ttype : str, optional "Typology" file type. build_topology : bool, optional Build the molecular topology consisting of: topology (overall connectivity graph), molecules (list of connected subgraphs), bonds (if not explicitly read in), default True toppbc : bool, optional Use periodic boundary conditions when building the molecular topology, default False The build_topology code will attempt to determine this intelligently. topframe : int, optional Provide a frame number for building the molecular topology, default first frame Fac : float, optional Multiplicative factor to covalent radii criterion for deciding whether two atoms are bonded Default value of 1.2 is reasonable, 1.4 will produce lots of bonds positive_resid : bool, optional If provided, enforce all positive resIDs.

Definition at line 1219 of file molecule.py.

Member Function Documentation

__add__()

def src.molecule.Molecule.__add__	(		self,
			other
	)

Add method for Molecule objects.

Definition at line 1496 of file molecule.py.

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__deepcopy__()

def src.molecule.Molecule.__deepcopy__	(		self,
			memo
	)

Custom deepcopy method because Python 3.6 appears to have changed its behavior.

Definition at line 1398 of file molecule.py.

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__delitem__()

def src.molecule.Molecule.__delitem__	(		self,
			key
	)

Similarly, in order to delete a frame, we simply perform item deletion on framewise variables.

Definition at line 1476 of file molecule.py.

__getattr__()

def src.molecule.Molecule.__getattr__	(		self,
			key
	)

Whenever we try to get a class attribute, it first tries to get the attribute from the Data dictionary.

Definition at line 1347 of file molecule.py.

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__getitem__()

def src.molecule.Molecule.__getitem__	(		self,
			key
	)

The Molecule class has list-like behavior, so we can get slices of it.

If we say MyMolecule[0:10], then we'll return a copy of MyMolecule with frames 0 through 9.

Definition at line 1453 of file molecule.py.

__iadd__()

def src.molecule.Molecule.__iadd__	(		self,
			other
	)

Add method for Molecule objects.

Definition at line 1543 of file molecule.py.

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__iter__()

def src.molecule.Molecule.__iter__

(

self

)

List-like behavior for looping over trajectories.

Note that these values are returned by reference. Note that this is intended to be more efficient than getitem, so when we loop over a trajectory, it's best to go "for m in M" instead of "for i in range(len(M)): m = M[i]"

Definition at line 1485 of file molecule.py.

__len__()

def src.molecule.Molecule.__len__

(

self

)

Return the number of frames in the trajectory.

Definition at line 1331 of file molecule.py.

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__setattr__()

def src.molecule.Molecule.__setattr__	(		self,
			key,
			value
	)

Whenever we try to get a class attribute, it first tries to get the attribute from the Data dictionary.

Definition at line 1386 of file molecule.py.

add_quantum()

def src.molecule.Molecule.add_quantum	(		self,
			other
	)

Definition at line 1813 of file molecule.py.

add_virtual_site()

def src.molecule.Molecule.add_virtual_site	(		self,
			idx,
			kwargs
	)

Add a virtual site to the system.

This does NOT set the position of the virtual site; it sits at the origin.

Definition at line 1826 of file molecule.py.

align()

def src.molecule.Molecule.align	(		self,
			smooth = False,
			center = True,
			center_mass = False,
			atom_select = None
	)

Align molecules.

Has the option to create smooth trajectories (align each frame to the previous one) or to align each frame to the first one.

Also has the option to remove the center of mass.

Provide a list of atom indices to align along selected atoms.

Definition at line 1994 of file molecule.py.

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align_by_moments()

def src.molecule.Molecule.align_by_moments

(

self

)

Align molecules using the moment of inertia.

Departs from MSMBuilder convention of using arithmetic mean for mass.

Definition at line 1952 of file molecule.py.

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align_center()

def src.molecule.Molecule.align_center

(

self

)

Definition at line 2854 of file molecule.py.

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aliphatic_hydrogens()

def src.molecule.Molecule.aliphatic_hydrogens

(

self

)

Definition at line 2791 of file molecule.py.

all_pairwise_rmsd()

def src.molecule.Molecule.all_pairwise_rmsd

(

self

)

Find pairwise RMSD (super slow, not like the one in MSMBuilder.)

Definition at line 2803 of file molecule.py.

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append()

def src.molecule.Molecule.append	(		self,
			other
	)

Definition at line 1652 of file molecule.py.

atom_select()

def src.molecule.Molecule.atom_select	(		self,
			atomslice,
			build_topology = True
	)

Return a copy of the object with certain atoms selected.

Takes an integer, list or array as argument.

Definition at line 1868 of file molecule.py.

atom_stack()

def src.molecule.Molecule.atom_stack	(		self,
			other
	)

Return a copy of the object with another molecule object appended.

WARNING: This function may invalidate stuff like QM energies.

Definition at line 1905 of file molecule.py.

build_bonds()

def src.molecule.Molecule.build_bonds

(

self

)

Build the bond connectivity graph.

Definition at line 2034 of file molecule.py.

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build_topology()

def src.molecule.Molecule.build_topology	(		self,
			force_bonds = True,
			kwargs
	)

Create self.topology and self.molecules; these are graph representations of the individual molecules (fragments) contained in the Molecule object.

Parameters

force_bonds : bool Build the bonds from interatomic distances. If the user calls build_topology from outside, assume this is the default behavior. If creating a Molecule object using init, do not force the building of bonds by default (only build bonds if not read from file.) topframe : int, optional Provide the frame number used for reading the bonds. If not provided, this will be taken from the top_settings field. If provided, this will take priority and write the value into top_settings.

Definition at line 2208 of file molecule.py.

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center()

def src.molecule.Molecule.center	(		self,
			center_mass = False
	)

Move geometric center to the origin.

Definition at line 2023 of file molecule.py.

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center_of_mass()

def src.molecule.Molecule.center_of_mass

(

self

)

Definition at line 1723 of file molecule.py.

distance_displacement()

def src.molecule.Molecule.distance_displacement

(

self

)

Obtain distance matrix and displacement vectors between all pairs of atoms.

Definition at line 2254 of file molecule.py.

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distance_matrix()

def src.molecule.Molecule.distance_matrix	(		self,
			pbc = True
	)

Obtain distance matrix between all pairs of atoms.

Definition at line 2242 of file molecule.py.

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edit_qcrems()

def src.molecule.Molecule.edit_qcrems	(		self,
			in_dict,
			subcalc = None
	)

Edit Q-Chem rem variables with a dictionary.

Pass a value of None to delete a rem variable.

Definition at line 1798 of file molecule.py.

find_angles()

def src.molecule.Molecule.find_angles

(

self

)

Return a list of 3-tuples corresponding to all of the angles in the system.

Verified for lysine and tryptophan dipeptide when comparing to TINKER's analyze program.

Definition at line 2502 of file molecule.py.

find_clashes()

def src.molecule.Molecule.find_clashes	(		self,
			thre = 0.0,
			pbc = True,
			groups = None
	)

Obtain a list of atoms that 'clash' (i.e.

are more than 3 bonds apart and are closer than the provided threshold.)

Parameters

thre : float Create a sorted-list of all non-bonded atom pairs with distance below this threshold pbc : bool Whether to use PBC when computing interatomic distances filt : tuple (group1, group2) If not None, only compute distances between atoms in 'group1' and atoms in 'group2'. For example this could be [gAtoms, oAtoms] from rotate_bond

Returns

minPair_frames : list of tuples The closest pair of non-bonded atoms in each frame minDist_frames : list of tuples The distance between the closest pair of non-bonded atoms in each frame clashPairs_frames : list of lists Pairs of non-bonded atoms with distance below the threshold in each frame clashDists_frames : list of lists Distances between pairs of non-bonded atoms below the threshold in each frame

Definition at line 2379 of file molecule.py.

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find_dihedrals()

def src.molecule.Molecule.find_dihedrals

(

self

)

Return a list of 4-tuples corresponding to all of the dihedral angles in the system.

Verified for alanine and tryptophan dipeptide when comparing to TINKER's analyze program.

Definition at line 2529 of file molecule.py.

find_rings()

def src.molecule.Molecule.find_rings	(		self,
			max_size = 6
	)

Return a list of rings in the molecule.

Tested on a DNA base pair and C60. Warning: Using large max_size for rings (e.g. for finding the macrocycle in porphyrin) could lead to some undefined behavior.

Parameters

max_size : int The maximum ring size. If a large ring contains smaller sub-rings, they are all mapped into one.

Returns

list A list of rings sorted in ascending order of the smallest atom number. The atoms in each ring are ordered starting from the lowest number and going along the ring, with the second atom being the lower of the two possible choices.

Definition at line 2621 of file molecule.py.

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get_populations()

def src.molecule.Molecule.get_populations

(

self

)

Return a cloned molecule object but with X-coordinates set to Mulliken charges and Y-coordinates set to Mulliken spins.

Definition at line 1966 of file molecule.py.

get_reaxff_atom_types()

def src.molecule.Molecule.get_reaxff_atom_types

(

self

)

Return a list of element names which maps the LAMMPS atom types to the ReaxFF elements.

Definition at line 4229 of file molecule.py.

load_frames()

def src.molecule.Molecule.load_frames	(		self,
			fnm,
			ftype = None,
			kwargs
	)

Definition at line 1769 of file molecule.py.

load_popxyz()

def src.molecule.Molecule.load_popxyz	(		self,
			fnm
	)

Given a charge-spin xyz file, load the charges (x-coordinate) and spins (y-coordinate) into internal arrays.

Definition at line 1977 of file molecule.py.

measure_angles()

def src.molecule.Molecule.measure_angles	(		self,
			i,
			j,
			k
	)

Definition at line 2560 of file molecule.py.

measure_dihedrals()

def src.molecule.Molecule.measure_dihedrals	(		self,
			i,
			j,
			k,
			l
	)

Return a series of dihedral angles, given four atom indices numbered from zero.

Definition at line 2575 of file molecule.py.

measure_distances()

def src.molecule.Molecule.measure_distances	(		self,
			i,
			j
	)

Definition at line 2551 of file molecule.py.

openmm_boxes()

def src.molecule.Molecule.openmm_boxes

(

self

)

Returns the periodic box vectors in the Molecule object in a list of OpenMM-compatible boxes, so it is possible to type simulation.context.setPeriodicBoxVectors(Mol.openmm_boxes()[0]) or something like that.

Definition at line 2880 of file molecule.py.

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openmm_positions()

def src.molecule.Molecule.openmm_positions

(

self

)

Returns the Cartesian coordinates in the Molecule object in a list of OpenMM-compatible positions, so it is possible to type simulation.context.setPositions(Mol.openmm_positions()[0]) or something like that.

Definition at line 2863 of file molecule.py.

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order_by_connectivity()

def src.molecule.Molecule.order_by_connectivity	(		self,
			m,
			i,
			currList,
			max_min_path
	)

Recursive function that orders atoms based on connectivity.

To call the function, pass in the topology object (e.g. M.molecules[0]) and the index of the atom assigned to be "first".

The neighbors of "i" are placed in decreasing order of the maximum length of the shortest path to all other atoms - i.e. an atom closer to the "edge" of the molecule has a longer shortest-path to atoms on the other "edge", and they should be added first.

Snippet:

from forcebalance.molecule import * import numpy as np M = Molecule('movProt.xyz', Fac=1.25)

Arbitrarily select heaviest atom as the first atom in each molecule

firstAtom = [m.L()[np.argmax([PeriodicTable[M.elem[i]] for i in m.L()])] for m in M.molecules]

Explicitly set the first atom in the first molecule

firstAtom[0] = 40

Build a list of new atom orderings

newOrder = [] for i in range(len(M.molecules)): newOrder += M.order_by_connectivity(M.molecules[i], firstAtom[i], [], None)

Write the new Molecule object

newM = M.atom_select(newOrder) newM.write('reordered1.xyz')

Parameters

m : topology object (contained in Molecule) i : integer Index of the atom to be added first (if called recursively, the index of subsequent atoms to be added) currList : list Current list of new atom orderings max_min_path : dict Dictionary mapping

Definition at line 2758 of file molecule.py.

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pathwise_rmsd()

def src.molecule.Molecule.pathwise_rmsd	(		self,
			align = True
	)

Find RMSD between frames along path.

Definition at line 2821 of file molecule.py.

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radius_of_gyration()

def src.molecule.Molecule.radius_of_gyration

(

self

)

Definition at line 1727 of file molecule.py.

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read_arc()

def src.molecule.Molecule.read_arc	(		self,
			fnm,
			kwargs
	)

Read a TINKER .arc file.

Parameters

[in]

fnm

The input file name

Returns

xyzs A list for the XYZ coordinates.

boxes A list of periodic boxes (newer .arc files have these)

resid The residue ID numbers. These are not easy to get!

elem A list of chemical elements in the XYZ file

comms A single-element list for the comment.

tinkersuf The suffix that comes after lines in the XYZ coordinates; this is usually topology info

Definition at line 3300 of file molecule.py.

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read_charmm()

def src.molecule.Molecule.read_charmm	(		self,
			fnm,
			kwargs
	)

Read a CHARMM .cor (or .crd) file.

Definition at line 3455 of file molecule.py.

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read_com()

def src.molecule.Molecule.read_com	(		self,
			fnm,
			kwargs
	)

Parse a Gaussian .com file and return a SINGLE-ELEMENT list of xyz coordinates (no multiple file support)

Parameters

[in]

fnm

The input file name

Returns

elem A list of chemical elements in the XYZ file

comms A single-element list for the comment.

xyzs A single-element list for the XYZ coordinates.

charge The total charge of the system.

mult The spin multiplicity of the system.

Definition at line 3255 of file molecule.py.

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read_comm_charge_mult()

def src.molecule.Molecule.read_comm_charge_mult	(		self,
			verbose = False
	)

Set charge and multiplicity from reading the comment line, formatted in a specific way.

Definition at line 2925 of file molecule.py.

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read_dcd()

def src.molecule.Molecule.read_dcd	(		self,
			fnm,
			kwargs
	)

Definition at line 3215 of file molecule.py.

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read_gro()

def src.molecule.Molecule.read_gro	(		self,
			fnm,
			kwargs
	)

Read a GROMACS .gro file.

Definition at line 3373 of file molecule.py.

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read_inpcrd()

def src.molecule.Molecule.read_inpcrd	(		self,
			fnm,
			kwargs
	)

Parse an AMBER .inpcrd or .rst file.

Parameters

[in]

fnm

The input file name

Returns

xyzs A list of XYZ coordinates (number of snapshots times number of atoms)

boxes Boxes (if present.)

Definition at line 3064 of file molecule.py.

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read_mdcrd()

def src.molecule.Molecule.read_mdcrd	(		self,
			fnm,
			kwargs
	)

Parse an AMBER .mdcrd file.

This requires at least the number of atoms. This will FAIL for monatomic trajectories (but who the heck makes those?)

Parameters

[in]

fnm

The input file name

Returns

xyzs A list of XYZ coordinates (number of snapshots times number of atoms)

boxes Boxes (if present.)

Definition at line 3031 of file molecule.py.

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read_mol2()

def src.molecule.Molecule.read_mol2	(		self,
			fnm,
			kwargs
	)

Definition at line 3161 of file molecule.py.

read_pdb()

def src.molecule.Molecule.read_pdb	(		self,
			fnm,
			kwargs
	)

Loads a PDB and returns a dictionary containing its data.

Definition at line 3649 of file molecule.py.

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read_qcesp()

def src.molecule.Molecule.read_qcesp	(		self,
			fnm,
			kwargs
	)

Definition at line 3746 of file molecule.py.

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read_qcin()

def src.molecule.Molecule.read_qcin	(		self,
			fnm,
			kwargs
	)

Read a Q-Chem input file.

These files can be very complicated, and I can't write a completely general parser for them. It is important to keep our goal in mind:

1) The main goal is to convert a trajectory to Q-Chem input files with identical calculation settings.

2) When we print the Q-Chem file, we should preserve the line ordering of the 'rem' section, but also be able to add 'rem' options at the end.

3) We should accommodate the use case that the Q-Chem file may have follow-up calculations delimited by '@@'.

4) We can read in all of the xyz's as a trajectory, but only the Q-Chem settings belonging to the first xyz will be saved.

Definition at line 3524 of file molecule.py.

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read_qcout()

def src.molecule.Molecule.read_qcout	(		self,
			fnm,
			errok = None,
			kwargs
	)

Q-Chem output file reader, adapted for our parser.

Q-Chem output files are very flexible and there's no way I can account for all of them. Here's what I am able to account for:

A list of:

• Coordinates
• Energies
• Forces

Calling with errok will proceed with reading file even if the specified error messages are encountered.

Note that each step in a geometry optimization counts as a frame.

As with all Q-Chem output files, note that successive calculations can have different numbers of atoms.

Definition at line 3778 of file molecule.py.

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read_qcschema()

def src.molecule.Molecule.read_qcschema	(		self,
			schema,
			kwargs
	)

Definition at line 2933 of file molecule.py.

read_qdata()

def src.molecule.Molecule.read_qdata	(		self,
			fnm,
			kwargs
	)

Definition at line 3125 of file molecule.py.

read_xyz()

def src.molecule.Molecule.read_xyz	(		self,
			fnm,
			kwargs
	)

.xyz files can be TINKER formatted which is why we have the try/except here.

Definition at line 2952 of file molecule.py.

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read_xyz0()

def src.molecule.Molecule.read_xyz0	(		self,
			fnm,
			kwargs
	)

Parse a .xyz file which contains several xyz coordinates, and return their elements.

Parameters

[in]

fnm

The input file name

Returns

elem A list of chemical elements in the XYZ file

comms A list of comments.

xyzs A list of XYZ coordinates (number of snapshots times number of atoms)

Definition at line 2967 of file molecule.py.

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ref_rmsd()

def src.molecule.Molecule.ref_rmsd	(		self,
			i,
			align = True
	)

Find RMSD to a reference frame.

Definition at line 2839 of file molecule.py.

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reorder_according_to()

def src.molecule.Molecule.reorder_according_to	(		self,
			other
	)

Reorder atoms according to some other Molecule object.

This happens when we run a program like pdb2gmx or pdbxyz and it scrambles our atom ordering, forcing us to reorder the atoms for all frames in the current Molecule object.

Directions: (1) Load up the scrambled file as a new Molecule object. (2) Call this function: Original_Molecule.reorder_according_to(scrambled) (3) Save Original_Molecule to a new file name.

Definition at line 1621 of file molecule.py.

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reorder_indices()

def src.molecule.Molecule.reorder_indices	(		self,
			other
	)

Return the indices that would reorder atoms according to some other Molecule object.

This happens when we run a program like pdb2gmx or pdbxyz and it scrambles our atom ordering.

Directions: (1) Load up the scrambled file as a new Molecule object. (2) Call this function: Original_Molecule.reorder_indices(scrambled)

Definition at line 1648 of file molecule.py.

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repair()

def src.molecule.Molecule.repair	(		self,
			key,
			klast
	)

Attempt to repair trivial issues that would otherwise break the object.

Definition at line 1586 of file molecule.py.

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replace_peratom()

def src.molecule.Molecule.replace_peratom	(		self,
			key,
			orig,
			want
	)

Replace all of the data for a certain attribute in the system from orig to want.

Definition at line 1845 of file molecule.py.

replace_peratom_conditional()

def src.molecule.Molecule.replace_peratom_conditional	(		self,
			key1,
			cond,
			key2,
			orig,
			want
	)

Replace all of the data for a attribute key2 from orig to want, contingent on key1 being equal to cond.

For instance: replace H1 with H2 if resname is SOL.

Definition at line 1857 of file molecule.py.

require()

def src.molecule.Molecule.require	(		self,
			args
	)

Definition at line 1656 of file molecule.py.

require_boxes()

def src.molecule.Molecule.require_boxes

(

self

)

Definition at line 4608 of file molecule.py.

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require_resid()

def src.molecule.Molecule.require_resid

(

self

)

Definition at line 4595 of file molecule.py.

require_resname()

def src.molecule.Molecule.require_resname

(

self

)

Definition at line 4603 of file molecule.py.

rigid_water()

def src.molecule.Molecule.rigid_water

(

self

)

If one atom is oxygen and the next two are hydrogen, make the water molecule rigid.

Definition at line 1739 of file molecule.py.

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rotate_bond()

def src.molecule.Molecule.rotate_bond	(		self,
			frame,
			aj,
			ak,
			increment = 15
	)

Return a new Molecule object containing the selected frame plus a number of frames where the selected dihedral angle is rotated in steps of 'increment' given in degrees.

This function is designed to be called by Molecule.rotate_check_clash().

Parameters

frame : int Structure number of the current Molecule to be rotated aj, ak : int Atom numbers of the bond to be rotated increment : float Degrees of the rotation increment

Returns

Molecule New Molecule object containing the rotated structures

Definition at line 2286 of file molecule.py.

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rotate_check_clash()

def src.molecule.Molecule.rotate_check_clash	(		self,
			frame,
			rotate_index,
			thresh_hyd = 1.4,
			thresh_hvy = 1.8,
			printLevel = 1
	)

Return a new Molecule object containing the selected frame plus a number of frames where the selected dihedral angle is rotated in steps of 'increment' given in degrees.

Additionally, check for if pairs of non-bonded atoms "clash" i.e. approach below the specified thresholds.

Parameters

frame : int Structure number of the current Molecule to be rotated (if only a single frame, this number should be 0) rotate_index : tuple 4 atom indices (ai, aj, ak, al) representing the dihedral angle to be rotated. The first and last indices are used to measure the dihedral angle. thresh_hyd : float Clash threshold for hydrogen atoms. Reasonable values are in between 1.3 and 2.0. thresh_hvy : float Clash threshold for heavy atoms. Reasonable values are in between 1.7 and 2.5. printLevel: int Sets the amount of printout (larger = more printout)

Returns

Molecule New Molecule object containing the rotated structures Success : bool True if no clashes

Definition at line 2445 of file molecule.py.

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split()

def src.molecule.Molecule.split	(		self,
			fnm = None,
			ftype = None,
			method = "chunks",
			num = None
	)

Split the molecule object into a number of separate files (chunks), either by specifying the number of frames per chunk or the number of chunks.

Only relevant for "trajectories". The type of file may be specified; if they aren't specified then the original file type is used.

The output file names are [name].[numbers].[extension] where [name] can be specified by passing 'fnm' or taken from the object's 'fnm' attribute by default. [numbers] are integers ranging from the lowest to the highest chunk number, prepended by zeros.

If the number of chunks / frames is not specified, then one file is written for each frame.

Returns

fnms A list of the file names that were written.

Definition at line 2903 of file molecule.py.

without()

def src.molecule.Molecule.without	(		self,
			args
	)

Return a copy of the Molecule object but with certain fields deleted if they exist.

This is useful for when we'd like to add Molecule objects that don't share some fields that we know about.

Definition at line 2915 of file molecule.py.

write()

def src.molecule.Molecule.write	(		self,
			fnm = None,
			ftype = None,
			append = False,
			selection = None,
			kwargs
	)

Definition at line 1678 of file molecule.py.

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write_arc()

def src.molecule.Molecule.write_arc	(		self,
			selection,
			kwargs
	)

Definition at line 4355 of file molecule.py.

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write_dcd()

def src.molecule.Molecule.write_dcd	(		self,
			selection,
			kwargs
	)

Definition at line 4404 of file molecule.py.

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write_gro()

def src.molecule.Molecule.write_gro	(		self,
			selection,
			kwargs
	)

Definition at line 4370 of file molecule.py.

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write_inpcrd()

def src.molecule.Molecule.write_inpcrd	(		self,
			selection,
			sn = None,
			kwargs
	)

Definition at line 4332 of file molecule.py.

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write_lammps_data()

def src.molecule.Molecule.write_lammps_data	(		self,
			selection,
			kwargs
	)

Write the first frame of the selection to a LAMMPS data file for the purpose of automatically initializing a LAMMPS simulation.

This function makes several assumptions until further notice:

(1) We are interested in a ReaxFF simulation (2) Atom types will be generated from elements

Definition at line 4245 of file molecule.py.

write_mdcrd()

def src.molecule.Molecule.write_mdcrd	(		self,
			selection,
			kwargs
	)

Definition at line 4321 of file molecule.py.

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write_molproq()

def src.molecule.Molecule.write_molproq	(		self,
			selection,
			kwargs
	)

Definition at line 4309 of file molecule.py.

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write_pdb()

def src.molecule.Molecule.write_pdb	(		self,
			selection,
			kwargs
	)

Definition at line 4430 of file molecule.py.

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write_qcin()

def src.molecule.Molecule.write_qcin	(		self,
			selection,
			kwargs
	)

Definition at line 4147 of file molecule.py.

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write_qdata()

def src.molecule.Molecule.write_qdata	(		self,
			selection,
			kwargs
	)

Text quantum data format.

Definition at line 4574 of file molecule.py.

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write_xyz()

def src.molecule.Molecule.write_xyz	(		self,
			selection,
			kwargs
	)

Definition at line 4213 of file molecule.py.

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Member Data Documentation

atomname

src.molecule.Molecule.atomname

Definition at line 4458 of file molecule.py.

boxes

src.molecule.Molecule.boxes

Definition at line 4658 of file molecule.py.

built_bonds

src.molecule.Molecule.built_bonds

Definition at line 1281 of file molecule.py.

charge

src.molecule.Molecule.charge

Definition at line 2927 of file molecule.py.

comms

src.molecule.Molecule.comms

Read in stuff if we passed in a file name, otherwise return an empty instance.

Fill in comments.

Try to determine from the file name using the extension. Actually read the file. Set member variables. Create a list of comment lines if we don't already have them from reading the file.

Definition at line 1311 of file molecule.py.

Data

src.molecule.Molecule.Data

Definition at line 1293 of file molecule.py.

fout

src.molecule.Molecule.fout

I needed to add in this line because the DCD writer requires the file name, but the other methods don't.

Definition at line 1692 of file molecule.py.

Funnel

src.molecule.Molecule.Funnel

A funnel dictionary that takes redundant file types and maps them down to a few.

Definition at line 1264 of file molecule.py.

molecules

src.molecule.Molecule.molecules

Definition at line 2235 of file molecule.py.

mult

src.molecule.Molecule.mult

Definition at line 2928 of file molecule.py.

positive_resid

src.molecule.Molecule.positive_resid

Creates entries like 'gromacs' : 'gromacs' and 'xyz' : 'xyz' in the Funnel.

Definition at line 1280 of file molecule.py.

qm_mulliken_charges

src.molecule.Molecule.qm_mulliken_charges

Definition at line 1979 of file molecule.py.

qm_mulliken_spins

src.molecule.Molecule.qm_mulliken_spins

Definition at line 1980 of file molecule.py.

Read_Tab

src.molecule.Molecule.Read_Tab

The table of file readers.

Definition at line 1235 of file molecule.py.

resid

src.molecule.Molecule.resid

Definition at line 4599 of file molecule.py.

resname

src.molecule.Molecule.resname

Definition at line 4606 of file molecule.py.

top_settings

src.molecule.Molecule.top_settings

Topology settings.

Definition at line 1283 of file molecule.py.

topology

src.molecule.Molecule.topology

Definition at line 2233 of file molecule.py.

Write_Tab

src.molecule.Molecule.Write_Tab

The table of file writers.

Definition at line 1251 of file molecule.py.

xyzs

src.molecule.Molecule.xyzs

Definition at line 4338 of file molecule.py.

---

The documentation for this class was generated from the following file:

• molecule.py