From f783ed0df373804a7c0122b18452e1499ca122aa Mon Sep 17 00:00:00 2001
From: pgbarletta <pbarletta@gmail.com>
Date: Wed, 20 Sep 2023 21:00:52 -0300
Subject: [PATCH] Fix charge reading from PDBQTParser

---
 package/CHANGELOG                                |   1 +
 package/MDAnalysis/coordinates/PDBQT.py          |   3 ++-
 package/MDAnalysis/topology/PDBQTParser.py       |   8 ++++++--
 testsuite/MDAnalysisTests/data/tyrosol.pdbqt.bz2 | Bin 0 -> 590 bytes
 testsuite/MDAnalysisTests/datafiles.py           |   2 ++
 testsuite/MDAnalysisTests/topology/test_pdbqt.py |   7 +++++++
 6 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 testsuite/MDAnalysisTests/data/tyrosol.pdbqt.bz2

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 1bb3abfd047..ffddbb0df54 100644
--- a/package/CHANGELOG
+++ b/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
diff --git a/package/MDAnalysis/coordinates/PDBQT.py b/package/MDAnalysis/coordinates/PDBQT.py
index c2523618b9a..41c1e97fc93 100644
--- a/package/MDAnalysis/coordinates/PDBQT.py
+++ b/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*.
     =============  ============  ===========  =============================================
 
diff --git a/package/MDAnalysis/topology/PDBQTParser.py b/package/MDAnalysis/topology/PDBQTParser.py
index eeebc889e2b..81a902fdcd8 100644
--- a/package/MDAnalysis/topology/PDBQTParser.py
+++ b/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)
diff --git a/testsuite/MDAnalysisTests/data/tyrosol.pdbqt.bz2 b/testsuite/MDAnalysisTests/data/tyrosol.pdbqt.bz2
new file mode 100644
index 0000000000000000000000000000000000000000..7a900995bb75d745b5128fd3177f3a013692bbb0
GIT binary patch
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diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py
index 25e85618afe..9a0c03561d4 100644
--- a/testsuite/MDAnalysisTests/datafiles.py
+++ b/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()
diff --git a/testsuite/MDAnalysisTests/topology/test_pdbqt.py b/testsuite/MDAnalysisTests/topology/test_pdbqt.py
index 2127617da05..f603400d9bc 100644
--- a/testsuite/MDAnalysisTests/topology/test_pdbqt.py
+++ b/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)
\ No newline at end of file