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Ethane: Reading from files, Ports and coordinate transforms¶
Note: mBuild expects all distance units to be in nanometers.
In this example, we’ll cover reading molecular components from files, introduce the concept of
Ports and start using some coordinate transforms.
First, we need to import the mbuild package:
import mbuild as mb
As you probably noticed while creating your methane molecule in the last tutorial, manually adding
Bonds to a
Compound is a bit cumbersome. The easiest way to create small, reusable components, such as methyls, amines or monomers, is to hand draw them using software like Avogadro and export them as either a .pdb or .mol2 file (the file should contain connectivity information).
Let’s start by reading a methyl group from a
import mbuild as mb ch3 = mb.load('ch3.pdb') ch3.visualize()
Now let’s use our first coordinate transform to center the methyl at its carbon atom:
import mbuild as mb ch3 = mb.load('ch3.pdb') mb.translate(ch3, -ch3.pos) # Move carbon to origin.
Now we have a methyl group loaded up and centered. In order to connect
Compounds in mBuild, we make use of a special type of
Port is a
Compound with two sets of four “ghost”
Particles. In addition
Ports have an
anchor attribute which typically points to a particle that the
Port should be associated with. In our methyl group, the
Port should be anchored to the carbon atom so that we can now form bonds to this carbon:
import mbuild as mb ch3 = mb.load('ch3.pdb') mb.translate(ch3, -ch3.pos) # Move carbon to origin. port = mb.Port(anchor=ch3) ch3.add(port, label='up') # Place the port at approximately half a C-C bond length. mb.translate(ch3['up'], [0, -0.07, 0])
Ports are never output from the mBuild structure. However, it can be useful to look at a molecule with the
Ports to check your work as you go:
Now we wrap the methyl group into a python class, so that we can reuse it as a component to build more complex molecules later.
import mbuild as mb class CH3(mb.Compound): def __init__(self): super(CH3, self).__init__() mb.load('ch3.pdb', compound=self) mb.translate(self, -self.pos) # Move carbon to origin. port = mb.Port(anchor=self) self.add(port, label='up') # Place the port at approximately half a C-C bond length. mb.translate(self['up'], [0, -0.07, 0])
Ports are connected, they are forced to overlap in space and their parent
Compounds are rotated and translated by the same amount.
Note: If we tried to connect two of our methyls right now using only one set of four ghost particles, not only would the
Ports overlap perfectly, but the carbons and hydrogens would also perfectly overlap - the 4 ghost atoms in the
Port are arranged identically with respect to the other atoms. For example, if a
Port and its direction is indicated by “<-“, forcing the port in <-CH3 to overlap with <-CH3 would just look like <-CH3 (perfectly overlapping atoms).
To solve this problem, every port contains a second set of 4 ghost atoms pointing in the opposite direction. When two
Compounds are connected, the port that places the anchor atoms the farthest away from each other is chosen automatically to prevent this overlap scenario.
When <->CH3 and <->CH3 are forced to overlap, the CH3<->CH3 is automatically chosen.
Now the fun part: stick ‘em together to create an ethane:
ethane = mb.Compound() ethane.add(CH3(), label="methyl_1") ethane.add(CH3(), label="methyl_2") mb.force_overlap(move_this=ethane['methyl_1'], from_positions=ethane['methyl_1']['up'], to_positions=ethane['methyl_2']['up'])
force_overlap() function takes a
Compound and then rotates and translates it such that two other
Compounds overlap. Typically, as in this case, those two other
Ports - in our case,
Similarly, if we want to make ethane a reusable component, we need to wrap it into a python class.
import mbuild as mb class Ethane(mb.Compound): def __init__(self): super(Ethane, self).__init__() self.add(CH3(), label="methyl_1") self.add(CH3(), label="methyl_2") mb.force_overlap(move_this=self['methyl_1'], from_positions=self['methyl_1']['up'], to_positions=self['methyl_2']['up'])
ethane = Ethane() ethane.visualize()
# Save to .mol2 ethane.save('ethane.mol2', overwrite=True)