hydrogen interaction formula + turns and bridges first implementation
Thomas Forest
parent
488dfa74a1
commit
e80fdb57ab
34
src/atom.py
34
src/atom.py
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@ -1,4 +1,12 @@
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import math
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class Atom:
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def dist_atoms(self, atom2):
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return(math.sqrt((self.coord_x-atom2.coord_x)**2 +
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(self.coord_y-atom2.coord_y)**2 +
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(self.coord_z-atom2.coord_z)**2))
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def __init__(self, atom_id, atom_name, res_name, chain_id,
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res_seq_nb, coordinates):
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self.atom_id = atom_id
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@ -15,5 +23,31 @@ class Residue:
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self.atoms = {}
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for atom in atoms_list:
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self.atoms[atom.atom_name] = atom
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self.resid = atom.res_seq_nb
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self.res_name = atom.res_name
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self.chain_id = atom.chain_id
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def h_bond(self, res2):
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if("H" not in res2.atoms.keys()):
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return(False)
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# elementary charge in Coulomb
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#e = 1.602176634 * 10*math.exp(-19)
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# dimensionnal factor f
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f = 332
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q1 = 0.42
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q2 = 0.20
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# r, distance between O-N atoms, in angströms
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r_ON = self.atoms["O"].dist_atoms(res2.atoms["N"])
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# r, distance between C-H atoms, in angströms
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r_CH = self.atoms["C"].dist_atoms(res2.atoms["H"])
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# r, distance between O-H atoms, in angströms
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r_OH = self.atoms["O"].dist_atoms(res2.atoms["H"])
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# r, distance between C-N atoms, in angströms
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r_CN = self.atoms["C"].dist_atoms(res2.atoms["N"])
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# Electrostatic interaction energy, in kcal/mole
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E = q1*q2*(1/r_ON + 1/r_CH - 1/r_OH - 1/r_CN)*f
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if(E<-0.5):
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return(True)
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else:
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return(False)
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@ -0,0 +1,18 @@
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import pdb
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import atom
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import sys
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from structure import *
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if(len(sys.argv)<2):
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print("Not enough arguments! Run with --help to learn more about proper"
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"call structure and parameters.")
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else:
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pdb_file = pdb.PDBFile(sys.argv[1])
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# print(pdb_file.residues[15].atoms["C"].coord_x)
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#print(pdb_file.residues[2].atoms["N"].res_seq_nb, pdb_file.residues[2].atoms["N"].coord_x, pdb_file.residues[2].atoms["N"].coord_y, pdb_file.residues[2].atoms["N"].coord_z)
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#print(pdb_file.residues[2].atoms["H"].coord_x)
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#print(pdb_file.residues[2].h_bond(pdb_file.residues[40]))
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#print(get_turns(pdb_file.residues))
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#print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
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get_bridges(pdb_file.residues)
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73
src/pdb.py
73
src/pdb.py
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@ -1,33 +1,33 @@
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# custom imports
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from atom import *
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# import libs
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import sys
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import pymol
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#import collections
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class PDBFile:
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def getContent(self, filename):
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def get_content(self, filename):
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with open(filename) as f:
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return(f.readlines())
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def getHeader(self):
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#Metadata = collections.namedtuple("Metadata", ["header", "compound", "source", "author"])
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Metadata = {}
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def get_header(self):
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metadata = {}
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for line in self.rawLines:
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# no need to continue if meta are complete
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if(len(Metadata) <4):
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if(len(metadata) <4):
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if(line[0:10] == "HEADER "):
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Metadata['header']=line
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metadata['header']=line
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elif(line[0:10] == "COMPND 2"):
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Metadata['compound']=line
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metadata['compound']=line
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elif(line[0:10] == "SOURCE 2"):
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Metadata['source']=line
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metadata['source']=line
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elif(line[0:10] == "AUTHOR "):
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Metadata['author']=line
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metadata['author']=line
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else:
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# if meta are complete, stop parsing
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break
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return(Metadata)
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return(metadata)
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def getAtoms(self, filename):
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def get_atoms(self, filename):
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self.atoms = []
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self.residues = []
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temp_atoms = []
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@ -56,10 +56,12 @@ class PDBFile:
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temp_atoms.append(atom)
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# last residue
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self.residues.append(Residue(temp_atoms))
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# hydrogens should represent in average 50% of total atoms... We use 30% threshold...
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# hydrogens should represent in average 50% of total atoms...
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# We use 30% threshold...
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if(count_h/len(temp_atoms)<0.30):
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#if(output_pdb==None):
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print("Need to add hydrogens ! If you want the modified PDB file, please use the -o output.pdb argument")
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print("Need to add hydrogens ! If you want the modified PDB file, "
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"please use the -o output.pdb argument")
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self.add_hydrogens(filename)
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def check_hydrogens(self, atoms):
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@ -71,25 +73,36 @@ class PDBFile:
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pymol.cmd.load(filename)
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pymol.cmd.select("nitrogens",'name n')
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pymol.cmd.h_add("nitrogens")
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pymol.stored.pos = []
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pymol.cmd.iterate_state(1, "hydrogens", 'stored.pos.append([name,resi,x,y,z])')
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pymol.stored.pos = {}
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pymol.cmd.iterate_state(1, "hydrogens",
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'stored.pos[resi] = []; ' \
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'stored.pos[resi].append(name,resi,x,y,z) '\
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'if resi not in stored.pos.keys() ' \
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'else ' \
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'stored.pos[resi].append([name,resi,x,y,z])')
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if(output_pdb!=None):
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pymol.cmd.save(output_file)
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for resi in self.residues:
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if(str(resi.resid) in pymol.stored.pos.keys()):
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# iterate over residue H atoms
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for hydrogen in pymol.stored.pos[str(resi.resid)]:
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atom = Atom(atom_id = len(self.atoms)+1,
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atom_name = "H",
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res_name = resi.res_name,
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chain_id = resi.chain_id,
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res_seq_nb = resi.resid,
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coordinates = [hydrogen[2],
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hydrogen[3],
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hydrogen[4]])
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# add hydrogen to atoms list
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self.atoms.append(atom)
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resi.atoms[atom.atom_name] = atom
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return(pymol.stored.pos)
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def __init__(self, filename, output_pdb=None):
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self.rawLines = self.getContent(filename)
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self.Metadata = self.getHeader()
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self.getAtoms(filename)
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# for elem in self.Metadata :
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# print(self.Metadata[elem], end="")
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self.rawLines = self.get_content(filename)
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self.metadata = self.get_header()
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self.get_atoms(filename)
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# for elem in self.metadata :
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# print(self.metadata[elem], end="")
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if __name__ == "__main__":
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if(len(sys.argv)<2):
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print("Not enough arguments! Run with --help to learn more about proper"
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"call structure and parameters.")
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else:
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pdbFile = PDBFile(sys.argv[1])
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print(pdbFile.residues[15].atoms["C"].coord_x)
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print(pdbFile.add_hydrogens(sys.argv[1])[3])
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@ -0,0 +1,49 @@
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class Turn:
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def __init__(self, turn_type):
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self.turn_type = turn_type
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class Bridge:
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def __init__(self, bridge_type):
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self.bridge_type = bridge_type
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class Helix:
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def __init__(self, residues):
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self.residues = residues
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def get_turns(residues):
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turns = []
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for i,res in enumerate(residues):
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for j in range(3,6):
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if(i+j<len(residues)):
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if(res.h_bond(residues[i+j])):
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turns.append(Turn(j))
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return(turns)
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def get_bridges(residues):
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# TODO : non-overlaping check to add
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bridges = []
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for i,res in enumerate(residues):
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for j, res in enumerate(residues):
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if(i-1>=0 and i+1<len(residues)
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and j-1>=0 and j+1<len(residues)):
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if((residues[i-1].h_bond(residues[j])
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and residues[j].h_bond(residues[i+1]))
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or(residues[j-1].h_bond(residues[i])
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and residues[i].h_bond(residues[j+1]))):
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bridges.append(Bridge("para"))
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if(i-1>=0 and i+1<len(residues)
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and j-1>=0 and j+1<len(residues)):
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if((residues[i].h_bond(residues[j])
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and residues[j].h_bond(residues[i]))
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or(residues[i-1].h_bond(residues[j+1])
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and residues[j-1].h_bond(residues[i+1]))):
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bridges.append(Bridge("anti"))
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return(bridges)
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def get_helix(turns):
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pass
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