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Add type checking for bond type.

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This commit is contained in:
Nathan Baker
2020-06-15 20:03:52 -07:00
parent 3dbc8c5217
commit 0703103cc1
1 changed files with 18 additions and 1 deletions
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19
pdb2pqr/pdb2pqr/ligand/mol2.py
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@@ -12,6 +12,10 @@ import numpy
_LOGGER = logging.getLogger(__name__)
# These are the allowed bond types
BOND_TYPES = {"single", "double", "aromatic"}
class Mol2Bond:
"""MOL2 molecule bonds."""
def __init__(self, atom1, atom2, bond_type, bond_id=0):
@@ -24,8 +28,12 @@ class Mol2Bond:
bond_id: integer ID of bond
"""
self.atoms = (atom1, atom2)
self.type = bond_type
self.bond_id = int(bond_id)
if bond_type in BOND_TYPES:
self.type = bond_type
else:
err = "Unknown bond type: %s" % bond_type
raise ValueError(err)
def __str__(self):
fmt = "{b.atoms[0]:s} {b.type:s}-bonded to {b.atoms[1]:s}"
@@ -306,6 +314,15 @@ class Mol2Molecule:
err = "Bond line too short: %s" % line
raise ValueError(err)
bond_type = words[3]
if bond_type == "1":
bond_type = "single"
elif bond_type == "2":
bond_type = "double"
elif bond_type == "ar":
bond_type = "aromatic"
else:
err = "Unknown bond type: %s" % bond_type
raise ValueError(err)
bond_id = int(words[0])
atom_id1 = int(words[1])
atom_id2 = int(words[2])