From 3329cb006353f049e88fb3f82708e3b2584de1fc Mon Sep 17 00:00:00 2001
From: diogom <diogom@scripps.edu>
Date: Fri, 26 Apr 2024 10:12:55 -0700
Subject: [PATCH] API CHANGE PDBQTReceptor init from string

---
 meeko/receptor_pdbqt.py | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/meeko/receptor_pdbqt.py b/meeko/receptor_pdbqt.py
index 12257ae6..b87ad3dd 100644
--- a/meeko/receptor_pdbqt.py
+++ b/meeko/receptor_pdbqt.py
@@ -99,7 +99,8 @@ def _read_receptor_pdbqt_string(pdbqt_string, skip_typing=False):
                               alt_id, in_code, occupancy, temp_factor, record_type))
 
             idx += 1
-
+    if idx == 0:
+        raise ValueError(f"no atoms found in {pdbqt_string=}") 
     atoms = np.array(atoms, dtype=atoms_dtype)
 
     return atoms, atom_annotations
@@ -129,23 +130,32 @@ class PDBQTReceptor:
     flexres_templates = flexres_templates
     skip_types=("H",)
 
-    def __init__(self, pdbqt_filename, skip_typing=False):
-        self._pdbqt_filename = pdbqt_filename
+    def __init__(self, pdbqt_string, skip_typing=False):
+        self._pdbqt_filename = None
         self._atoms = None
         self._atom_annotations = None
         self._KDTree = None
 
-        with open(pdbqt_filename) as f:
-            pdbqt_string = f.read()
-
         self._atoms, self._atom_annotations = _read_receptor_pdbqt_string(pdbqt_string, skip_typing)
         # We add to the KDTree only the rigid part of the receptor
         self._KDTree = spatial.cKDTree(self._atoms['xyz'])
         self._bonds = _identify_bonds(self._atom_annotations['all'], self._atoms['xyz'], self._atoms['atom_type'])
         self.atom_idxs_by_res = self.get_atom_indices_by_residue(self._atoms)
 
+    @classmethod
+    def from_pdbqt_filename(cls, pdbqt_filename, skip_typing=False):
+        with open(pdbqt_filename) as f:
+            pdbqt_string = f.read()
+        receptor = cls(pdbqt_string, skip_typing)
+        receptor._pdbqt_filename = pdbqt_filename
+        return receptor
+
     def __repr__(self):
-        return ('<Receptor from PDBQT file %s containing %d atoms>' % (self._pdbqt_filename, self._atoms.shape[0]))
+        if self._pdbqt_filename is None:
+            msg = '<Receptor containing %d atoms>' % self._atoms.shape[0]
+        else:
+            msg ='<Receptor from PDBQT file %s containing %d atoms>' % (self._pdbqt_filename, self._atoms.shape[0])
+        return msg
 
     @staticmethod
     def get_atom_indices_by_residue(atoms):