Fix charge reading from PDBQTParser

package/CHANGELOG

@@ -27,6 +27,7 @@ Fixes
   * Fixes a case where qcprot.CalcRMSDRotationalMatrix would return a
     RMSD of None
   * Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
+  * Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)
 
 Enhancements
   * Updated lib.qcprot.CalcRMSDRotationalMatrix to accept either float32 or float64

package/MDAnalysis/coordinates/PDBQT.py

@@ -87,7 +87,8 @@ class PDBQTReader(base.SingleFrameReaderBase):
     47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
     55 - 60        Real(6.2)     occupancy    Occupancy.
     61 - 66        Real(6.2)     tempFactor   Temperature  factor.
-    67 - 76        Real(10.4)    partialChrg  Gasteiger PEOE partial charge *q*.
+    67 - 70        LString(4)    footnote     Usually blank. IGNORED.
+    71 - 76        Real(6.4)     partialChrg  Gasteiger PEOE partial charge *q*.
     79 - 80        LString(2)    atomType     AutoDOCK atom type *t*.
     =============  ============  ===========  =============================================
 

package/MDAnalysis/topology/PDBQTParser.py

@@ -98,11 +98,15 @@ class PDBQTParser(TopologyReaderBase):
      - charges
 
     Guesses the following:
-     - elements
      - masses
 
     .. versionchanged:: 0.18.0
        Added parsing of Record types
+    .. versionchanged:: 2.7.0
+       Columns 67 - 70 in ATOM records, corresponding to the field *footnote*,
+       are now ignored. See Autodock's `reference`_.
+
+       .. _reference: https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf
     """
     format = 'PDBQT'
 
@@ -141,7 +145,7 @@ def parse(self, **kwargs):
                 icodes.append(line[26:27].strip())
                 occupancies.append(float(line[54:60]))
                 tempfactors.append(float(line[60:66]))
-                charges.append(float(line[66:76]))
+                charges.append(float(line[70:76]))
                 atomtypes.append(line[77:80].strip())
 
         n_atoms = len(serials)

testsuite/MDAnalysisTests/datafiles.py

@@ -123,6 +123,7 @@
     "PQR_icodes",  # PQR v2 with icodes
     "PDBQT_input",  # PDBQT
     "PDBQT_querypdb",
+    "PDBQT_tyrosol",
     "PDB_multipole",
     "FASTA",  # sequence alignment, Issue 112 + 113
     "HELANAL_BENDING_MATRIX",  # HELANAL test (from PSF+DCD (AdK) helix 8)
@@ -476,6 +477,7 @@
 
 PDBQT_input = (_data_ref / 'pdbqt_inputpdbqt.pdbqt').as_posix()
 PDBQT_querypdb = (_data_ref / 'pdbqt_querypdb.pdb').as_posix()
+PDBQT_tyrosol = (_data_ref / 'tyrosol.pdbqt.bz2').as_posix()
 
 FASTA = (_data_ref / 'test.fasta').as_posix()
 HELANAL_BENDING_MATRIX = (_data_ref / 'helanal_bending_matrix_AdK_DIMS_H8.dat').as_posix()

testsuite/MDAnalysisTests/topology/test_pdbqt.py

@@ -25,6 +25,7 @@
 from MDAnalysisTests.topology.base import ParserBase
 from MDAnalysisTests.datafiles import (
     PDBQT_input,  # pdbqt_inputpdbqt.pdbqt
+    PDBQT_tyrosol, # tyrosol.pdbqt.bz2
 )
 
 
@@ -50,3 +51,9 @@ class TestPDBQT(ParserBase):
     expected_n_atoms = 1805
     expected_n_residues = 199  # resids go 2-102 then 2-99
     expected_n_segments = 2  # res2-102 are A, 2-99 are B
+
+def test_footnote():
+    """just test that the Universe is built even in the presence of a
+    footnote before the charges.
+    """
+    mda.Universe(PDBQT_tyrosol)