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Pymol silent mode and hydrogen_add threshold

master
Thomas Forest 2019-09-13 00:30:32 +02:00
parent ea766855d7
commit 488dfa74a1
1 changed files with 19 additions and 13 deletions
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32
src/pdb.py
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@ -1,7 +1,7 @@
# custom imports # custom imports
from atom import * from atom import *
import sys import sys
import pymol import pymol
#import collections #import collections
class PDBFile: class PDBFile:
def getContent(self, filename): def getContent(self, filename):
@ -27,12 +27,15 @@ class PDBFile:
break break
return(Metadata) return(Metadata)
def getAtoms(self): def getAtoms(self, filename):
self.atoms = [] self.atoms = []
self.residues = [] self.residues = []
temp_atoms = [] temp_atoms = []
count_h = 0
for line in self.rawLines: for line in self.rawLines:
if line.startswith("ATOM" or "HETATM"): if line.startswith("ATOM" or "HETATM"):
if(line[76:78].strip()=="H"):
count_h+=1
atom = Atom(atom_id = int(line[6:11].strip()), atom = Atom(atom_id = int(line[6:11].strip()),
atom_name = line[12:16].strip(), atom_name = line[12:16].strip(),
res_name = line[17:20].strip(), res_name = line[17:20].strip(),
@ -53,17 +56,23 @@ class PDBFile:
temp_atoms.append(atom) temp_atoms.append(atom)
# last residue # last residue
self.residues.append(Residue(temp_atoms)) self.residues.append(Residue(temp_atoms))
# hydrogens should represent in average 50% of total atoms... We use 30% threshold...
if(count_h/len(temp_atoms)<0.30):
#if(output_pdb==None):
print("Need to add hydrogens ! If you want the modified PDB file, please use the -o output.pdb argument")
self.add_hydrogens(filename)
def check_hydrogens(self, atoms): def check_hydrogens(self, atoms):
return true print("ENTER CHECK HYDROGEN")
return True
def add_hydrogens(self, filename, output_pdb=None): def add_hydrogens(self, filename, output_pdb=None):
pymol.finish_launching(['pymol', '-qc'])
pymol.cmd.load(filename) pymol.cmd.load(filename)
pymol.cmd.select("nitrogens", selection='name n') pymol.cmd.select("nitrogens",'name n')
pymol.cmd.h_add("nitrogens") pymol.cmd.h_add("nitrogens")
pymol.cmd.select('hydrogens',selection='name h')
pymol.stored.pos = [] pymol.stored.pos = []
pymol.cmd.iterate_state(1, 'hydrogens', 'stored.pos.append([name,resi,x,y,z])') pymol.cmd.iterate_state(1, "hydrogens", 'stored.pos.append([name,resi,x,y,z])')
if(output_pdb!=None): if(output_pdb!=None):
pymol.cmd.save(output_file) pymol.cmd.save(output_file)
return(pymol.stored.pos) return(pymol.stored.pos)
@ -71,13 +80,10 @@ class PDBFile:
def __init__(self, filename, output_pdb=None): def __init__(self, filename, output_pdb=None):
self.rawLines = self.getContent(filename) self.rawLines = self.getContent(filename)
self.Metadata = self.getHeader() self.Metadata = self.getHeader()
self.getAtoms() self.getAtoms(filename)
for elem in self.Metadata : # for elem in self.Metadata :
print(self.Metadata[elem], end="") # print(self.Metadata[elem], end="")
if(self.check_hydrogens(self.atoms)==False):
if(output_pdb==None):
print("Need to add hydrogens ! If you want the modified PDB file, please use the -o output.pdb argument")
self.add_hydrogens(filename)
if __name__ == "__main__": if __name__ == "__main__":
if(len(sys.argv)<2): if(len(sys.argv)<2):