In [1]:
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
In [2]:
# real test case
In [3]:
pdb = PDBFile("/Users/weilu/Research/server/jan_2020/include_small_molecular/my_ABCDE_with_ligand/my_ABCDE_with_ligand-openmmawsem.pdb")
In [10]:
def dis(pos1, pos2):
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
return r
In [5]:
res_list = list(pdb.topology.residues())
atom_list = list(pdb.topology.atoms())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
In [6]:
info = []
for res in ligand_res_list:
atoms = list(res.atoms())
n_atoms = len(atoms)
for i in range(n_atoms):
atom1 = atoms[i]
pos1 = pdb.positions[atom1.index]
for j in range(i+1, n_atoms):
atom2 = atoms[j]
pos2 = pdb.positions[atom2.index]
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
# print(atom1.index, atom2.index, round(r, 3))
info.append([res.name, atom1.index, atom2.index, atom1.name, atom2.name, atom1.element.symbol, atom2.element.symbol, round(r, 3)])
In [7]:
import pandas as pd
data = pd.DataFrame(info, columns=["Name", "Atom1", "Atom2", "Name1", "Name2", "Symbol1", "Symbol2", "r"])
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forcefield = ForceField("/Users/weilu/openmmawsem/awsem.xml")
[templates, names] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
for a in templates:
for a1 in a.atoms:
if a1.element.symbol == "C":
a1.type = "CA"
else:
a1.type = a1.element.symbol
# a1.type = a1.element.symbol
forcefield.registerResidueTemplate(a)
system = forcefield.createSystem(pdb.topology)
In [15]:
info = []
for ligand_atom in ligand_atom_list:
pos1 = pdb.positions[ligand_atom.index]
for protein_atom in protein_atom_list:
if protein_atom.name != "CB":
continue
protein_chain = protein_atom.residue.chain.id
pos2 = pdb.positions[protein_atom.index]
r = dis(pos1, pos2)
if r < 0.65:
# print(ligand_atom, protein_atom, "in contact", r)
info.append([ligand_atom.index, protein_atom.index, r, protein_chain])
In [16]:
data = pd.DataFrame(info, columns=["Ligand_atom_index", "Protein_atom_index", "r", "Protein_chain"])
In [21]:
without_E = data.query("Protein_chain != 'E'").reset_index(drop=True)
without_E.to_csv("/Users/weilu/Research/server/jan_2020/include_small_molecular/het_protein_bonds_without_chainE.csv", index=False)
In [130]:
data.to_csv("/Users/weilu/Research/server/jan_2020/include_small_molecular/het_protein_bonds.csv", index=False)
In [133]:
data = pd.read_csv("/Users/weilu/Research/server/jan_2020/include_small_molecular/het_protein_bonds.csv")
In [134]:
data.dtypes
Out[134]:
In [127]:
protein_atom_list[0]
Out[127]:
In [23]:
res.
Out[23]:
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atom.name
Out[123]:
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d = pdb.positions[atom.index]
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atom = ligand_atom_list[0]
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atom.index
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a = list(pdb.getTopology().bonds())
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a = ligand_atom_list[0]
In [103]:
ligand_atoms_index_list = [atom.index for atom in ligand_atom_list]
protein_atoms_index_list = [atom.index for atom in protein_atom_list]
In [106]:
a = protein_atom_list[0]
In [108]:
Out[108]:
In [96]:
atom1 = a[0].atom1
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atom1.index
Out[97]:
In [98]:
atom1.id
Out[98]:
In [128]:
pdb.getTopology()
Out[128]:
In [4]:
forcefield = ForceField("/Users/weilu/openmmawsem/awsem.xml")
In [5]:
[templates, names] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
In [6]:
for a in templates:
for a1 in a.atoms:
if a1.element.symbol == "C":
a1.type = "CA"
else:
a1.type = a1.element.symbol
# a1.type = a1.element.symbol
forcefield.registerResidueTemplate(a)
In [7]:
system = forcefield.createSystem(pdb.topology)
In [8]:
a = templates[0]
In [61]:
names
Out[61]:
In [10]:
res_list = list(pdb.topology.residues())
atom_list = list(pdb.topology.atoms())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
In [11]:
ligand_res_list
Out[11]:
In [15]:
positions = pdb.positions
In [46]:
atoms = list(res.atoms())
In [48]:
atom = atoms[0]
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atom.index
Out[49]:
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atom1.name
Out[68]:
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atom.element.symbol
Out[69]:
In [81]:
info = []
for res in ligand_res_list:
atoms = list(res.atoms())
n_atoms = len(atoms)
for i in range(n_atoms):
atom1 = atoms[i]
pos1 = pdb.positions[atom1.index]
for j in range(i+1, n_atoms):
atom2 = atoms[j]
pos2 = pdb.positions[atom2.index]
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
# print(atom1.index, atom2.index, round(r, 3))
info.append([res.name, atom1.index, atom2.index, atom1.name, atom2.name, atom1.element.symbol, atom2.element.symbol, round(r, 3)])
In [82]:
In [83]:
import pandas as pd
data = pd.DataFrame(info, columns=["Name", "Atom1", "Atom2", "Name1", "Name2", "Symbol1", "Symbol2", "r"])
In [84]:
data
Out[84]:
In [85]:
data.to_csv("/Users/weilu/Research/server/jan_2020/include_small_molecular/het_frag.csv", index=False)
In [79]:
for i, line in data.iterrows():
atom1 = line["Atom1"]
atom2 = line["Atom2"]
r = float(line["r"])
print(atom1, atom2, r)
In [16]:
len(positions)
Out[16]:
In [52]:
pos1 = positions[3548]
In [53]:
pos2 = positions[3551]
In [54]:
(pos1[0]**2 + pos1[1]**2 + pos1[2]**2)**0.5
Out[54]:
In [55]:
dis = pos1 - pos2
dis = dis.value_in_unit(nanometer)
r = (dis[0]**2 + dis[1]**2 + dis[2]**2)**0.5
In [56]:
r
Out[56]:
In [17]:
res = ligand_res_list[0]
In [18]:
b = list(res.bonds())[0]
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b.atom1
Out[19]:
In [20]:
list(res.bonds())
Out[20]:
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b.type
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atom1 = b.atom1
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atom1.id
Out[162]:
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atom1.index
Out[163]:
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atom1.element.symbol
Out[168]:
In [ ]:
# initial testing.
In [5]:
origin_pdb = PDBFile("/Users/weilu/Research/server/jan_2020/include_small_molecular/6ud8_F_complete/6ud8_F_complete-openmmawsem.pdb")
In [6]:
origin_pdb.getTopology()
Out[6]:
In [64]:
pdb = PDBFile("/Users/weilu/Research/server/jan_2020/include_small_molecular/6ud8_F_complete-openmmawsem.pdb")
In [65]:
pdb.getTopology()
Out[65]:
In [66]:
forcefield = ForceField("/Users/weilu/openmmawsem/awsem.xml")
In [67]:
forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
Out[67]:
In [68]:
[template, ffxml] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
In [69]:
a = template[0]
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a.name
Out[70]:
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a.bonds
Out[71]:
In [56]:
a
Out[56]:
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for a1 in a.atoms:
a1.type = a1.element.symbol
In [72]:
a1 = a.atoms[0]
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a1.element.symbol
Out[73]:
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a1.name
Out[74]:
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a1.parameters
Out[75]:
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a1.type
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a1.externalBonds
Out[77]:
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a.externalBonds
Out[78]:
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a1.bondedTo
Out[80]:
In [82]:
a.atoms[3].name
Out[82]:
In [21]:
olc = a[1]
In [40]:
forcefield.getGenerators()
Out[40]:
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forcefield.registerResidueTemplate(a)
In [89]:
system = forcefield.createSystem(pdb.topology)
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system.getNumParticles()
Out[90]:
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system.
Out[126]:
In [95]:
b = list(pdb.topology.atoms())
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b[-1]
Out[96]:
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b[0]
Out[97]:
In [103]:
b0 = b[-1]
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b0.id
Out[104]:
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b0.index
Out[105]:
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b0.element
Out[106]:
In [107]:
pdb.topology.getNumResidues()
Out[107]:
In [111]:
res_list = list(pdb.topology.residues())
protein_resNames = ["NGP", "IGL", "IPR", "NTER", "CTER"]
DNA_resNames = ["DA", "DC", "DT", "DG"]
protein_res_list = []
DNA_res_list = []
ligand_res_list = []
for res in res_list:
if res.name in protein_resNames:
protein_res_list.append(res)
elif res.name in DNA_resNames:
DNA_res_list.append(res)
else:
ligand_res_list.append(res)
In [112]:
res = res_list[0]
In [114]:
In [ ]:
nres = len(protein_res_list)
residues = protein_res_list
natoms
In [117]:
atom_list = list(pdb.topology.atoms())
In [124]:
protein_atom_list = []
DNA_atom_list = []
ligand_atom_list = []
for atom in atom_list:
if atom.residue.name in protein_resNames:
protein_atom_list.append(atom)
elif atom.residue.name in DNA_resNames:
DNA_atom_list.append(atom)
else:
ligand_atom_list.append(atom)
In [119]:
atom = atom_list[0]
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ligand_atom_list
Out[125]:
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atom.index
Out[120]:
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atom.name
Out[121]:
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atom.residue.name
Out[123]:
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DNA_res_list
Out[116]:
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ligand_res_list
Out[115]:
In [ ]:
for res in res_list:
if