Pose

A bare metal Python library for building and manipulating protein molecular structures

Description:

This library constructs a pose for a protein molecule, which is a data structure for that contains relevant information that defines the polypeptide molecule. Primary information includes the XYZ cartesian coordinates of each atom, the identify and charge of each atom, and the bond graph of the entire molecule, as well as other secondary information such as the FASTA sequence of the molecule, the molecule's radius of gyration, potential energy, and the secondary structure that each amino acid belongs to.

Using this information, the pose can build (canonical and non-canonical amino acids, including both L-amino acids and D-amino acids) and manipulate polypeptides, such as building any polypeptide from sequence, move the torsion and rotamer angles, mutate residues, as well as measure the bond lengths and angles. This data structure can be used to build higher level protocols such as simulated annealing, and machine learning-based protein design.

Note It is important to note that this library uses zero-based array indexing, NOT one-based array indexing as is in the PDB. It is thus important to note that the first amino acid and the first atom is indexed as 0 and not 1.

List of available amino acids:

A - ALA	B - LYX	C - CYS	D - ASP	E - GLU	F - PHE	G - GLY	H - HIS	I - ILE	J - MSE
K - LYS	L - LEU	M - MET	N - ASN	O - PYL	P - PRO	Q - GLN	R - ARG	S - SER	T - THR
U - SEC	V - VAL	W - TRP	X - TRF	Y - TYR	Z - TSO

Installation:

For pip:

pip install git+https://github.com/sarisabban/Pose

For anaconda:

conda create -n ENVIRONMENT python=3
conda activate ENVIRONMENT
pip3 install git+https://github.com/sarisabban/Pose

Example code:

from pose import *

pose = Pose()
pose.Build('SaRi')
pose.Export('output.pdb')

Note Capital letter unicodes will build L-amino acids, small letter unicodes will build D-amino acids.

Description of the AminoAcid.json:

Dictionary Key	Value Type	Description of Values
Vectors	List of lists	The position of each atom relative to the N of the backbone. If the N coorinate is X, Y, Z = 0, 0, 0 you will get these vectors. To find the correct vectors position the N at coordinate X, Y, Z = 0, 0, 0, and use the corresponding coordinates of each atom
Tricode	String	The three letter code for each amino acid
Atoms	List of lists	The atom identity of each coordinate point, first coordinate point is the nitrogen with symbol N and PDB entry N, next atom is the hydrogen that is bonded to the nitrogen with symbol H and PDB entry 1H etc... Unlike the PDB where all hydrogens are collected after the amino acid, here each atom's hydrogens come right after it. This makes for easier matrix operations. Order is index [0] == PDB atom's name, index [1] == element, index [2] == charge, index [3] == temperature factor
Chi Angle Atoms	List of lists	The atoms in the sidechain that are contributing to a chi angle
Bonds	Dictionary	The bond graph as an adjacency list

Description of the polypeptide's data structure:

Dictionary Key	Value Type	Description of Values
Energy	Float	The potential energy of the molecule
Rg	Float	The radius of gyration of the molecule
Mass	Float	The mass of the molecule in Daltons
Size	Integer	The sequence length of the molecule
FASTA	String	The FASTA sequence of the molecule
Amino Acids	Dictionary	The key is the index in sequence, the value is the amino acid symbol, chain, backbone atom indices, sidechain atom indices, and the secondary structure the amino acid belongs to
Atoms	Dictionary	The key is the index in the coordinates matrix, the value is the atom's PDB symbol, the element symbol, the charge, and the temperature factor
Bonds	Dictionary	The bond graph of the molecule as an adjacency list
Coordinates	Numpy array	The XYZ cartesian coordinates of each atom

Table of methods:

Method	Description with example
pose = Pose()	Construct the Pose class
pose.Build('SARI')	Build a polypeptide using a sequence, the polypeptide will be in primary structure. Example: the sequence 'SARI'. Capital letters for L-amino acids, small letters for D-amino acids
pose.Import('1tqg.pdb', chain='A')	Import a structure from a .pdb file specifically chain 'A' of the complex (if no hydrogens are in the PDB they will not be added). To add Hydrogens use pose.ReBuild() after pose.Import() to re-build the structure with Hydrogens (there will be slight variation in the sidechains). Cannot use structures with broken non-continuous chains
pose.ReBuild()	Build the sequence of the polypeptide it as a primary structure then re-fold it using its amino acid angles and bond lengths
pose.Export('out.pdb')	Export the polypeptide to a .pdb file. Example: the output file's name is out.pdb
pose.Mutate(1, 'V')	Mutate an amno acid. Example: Mutate second amino acid to become Valine
pose.Angle(2, 'chi', 1)	Get the PHI, PSI, OMEGA, or CHI 1-4 angles of an amino acid. Example: second amino acid's CHI 1 angle. For the PHI, PSI, and OMEGA angles no need to include the second argument (the 1 in this example)
pose.Rotate(2, 20, 'chi', 1)	Change an angle to reach a degrees. Example: third amino acid, change angle to become 20 degrees, the angle type is CHI 1
pose.Atom3Angle(0, 'N', 0, 'CA', 0, 'C')	Get the angle between any three atoms in any amino acid. Example: first amino acid's Nitrogen, first amino acid's Carbon alpha, and first amino acid's Carbon
pose.Rotation3Angle(1, 'N', 1, 'CA', 1, 'C', -2)	Add/Subtract any three atom backbone angle from current degrees. Example: second amino acid, subtract 2 degrees from the N-Ca-C angle
pose.Distance(0, 'N', 1, 'CA')	Get the distance (in Å) between any two atoms in any amino acid. Example: distance between first amino acid's Nitrogen atom and second amino acid's Carbon alpha atom
pose.Adjust(0, 'N', 0, 'CA', 10)	Adjust the distance between any two atoms in any amno acid. Example: distance between first amino acid's Nitrogen and first amino acid's Carbon alpha to become 10 Å. The order of the atoms makes a difference, (0, 'N', 0, 'CA', 10) ≠ (0, 'CA', 0, 'N', 10), useful to seperate the chain behind the N
pose.GetBondAtoms(0, 1)	Get the atom pair that participate in a bond from their index. Example: atom index 0 and atom index 1 return ['N', 'N', 'HA', 'H'], this returns both atom's PDB name and the element's name
pose.GetAtom(3, 'N')	Get XYZ cartesian coordinates of an atom. Example: fourth amino acid's Nitrogen atom
pose.AtomList(PDB=True)	Get a list of all the atoms in the polypeptide, use PDB=True to get their PDB formatted names
pose.Identify(3, 'atom', q=True)	Identify what 'atom' type belongs to a particular index in the coordinates matrix, use q=True to identify the atom's charge, use 'residue' or 'amino acid' to instead identify the amino acid by index in the polypeptide sequence
pose.SecondaryStructures()	Get a list of each amino acid's secondary structure H:Helix, S:Sheet, L:Loop
pose.Info()	Print all the information about the polypeptide in an organised printout
print(pose.data)	Print the dictionary data structure where all the polypeptide's information reside

For collaboration:

If anyone is interested in collaborating and contributing, these are functions that needs to be added:

1. Easy: update Rebuild() to rebuild a structure but with all D-AAs. (how to modify the Phi/Psi angles)?
2. Easy: Structure alignment (RMSD between two poses)
3. Easy: Sequence alignment (BLAST & MSA)
4. Moderate: Calculating Gasteiger partial charges for each atom
5. Moderate: Find all H-bonds
6. Moderate: Calculate DSSP for each amino acid
7. Hard: SASA calculation for each amino acid
8. Hard: Pocket and void calculation
9. Hard: AMBER energy function + Minimisation