Fix invalid escape sequences

scripts/ccp4_contact.py

@@ -23,13 +23,14 @@
     AUTHOR
         Gerhard Reitmayr and Dalia Daujotyte, 2011.
 '''
+from pathlib import Path
 from pymol import cmd
 import re
 
 
 def parseCONTACTContacts(f):
     # Lys    24A  ca  Asp   263D  CG   ...  4.94    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
-    conParser = re.compile("(\S*)\s*(\d+)([A-Z])\s*(\w+)")
+    conParser = re.compile(r"(\S*)\s*(\d+)([A-Z])\s*(\w+)")
     s1 = []
     s2 = []
     for line in f:
@@ -73,3 +74,14 @@ def ccp4_contact(contactsfile, selName1="source", selName2="target"):
     cmd.select(selName2 + "_atom", atomSel)
 
 cmd.extend("ccp4_contact", ccp4_contact)
+
+
+def test_ccp4_contact():
+    datadir = Path(__file__).parents[1] / "files_for_examples"
+    cmd.reinitialize()
+    cmd.fab("PCQAFSISGKQKGFEDSRGTL", chain="A", resi=80)
+    ccp4_contact(f"{datadir}/2c7r.contact", selName1="sel1", selName2="sel2")
+    assert cmd.count_atoms("sel1_res") == 128
+    assert cmd.count_atoms("sel1_atom") == 20
+    assert cmd.count_atoms("sel2_res") == 128
+    assert cmd.count_atoms("sel2_atom") == 20

scripts/ccp4_ncont.py

@@ -23,15 +23,15 @@
     AUTHOR
         Gerhard Reitmayr and Dalia Daujotyte, 2009.
 '''
-from __future__ import print_function
+from pathlib import Path
 from pymol import cmd
 import re
 
 
 def parseNCONTContacts(f):
     # /1/B/ 282(PHE). / CE1[ C]:  /1/E/ 706(GLN). / O  [ O]:   3.32
     # * in the second group is needed when chain code is blank
-    conParser = re.compile("\s*/(\d+)/([a-zA-Z0-9]*)/\s*(\d+).*?/\s*([a-zA-Z0-9]*).*?:")
+    conParser = re.compile(r"\s*/(\d+)/([a-zA-Z0-9]*)/\s*(\d+).*?/\s*([a-zA-Z0-9]*).*?:")
     mode = 0
     s1 = []
     s2 = []
@@ -83,3 +83,21 @@ def ccp4_ncont(contactsfile, selName1="source", selName2="target"):
     cmd.select(selName2 + "_atom", atomSel)
 
 cmd.extend("ccp4_ncont", ccp4_ncont)
+
+
+def test_ccp4_ncont():
+    datadir = Path(__file__).parents[1] / "files_for_examples"
+    cmd.reinitialize()
+    cmd.fab("PCQAFSISGKQKGFEDSRGTL", "m1", chain="A", resi=80)
+    cmd.fnab("GCTGAC", "m2", dbl_helix=False)
+    cmd.remove("hydro")
+    cmd.alter("m2", "chain = 'C'")
+    cmd.alter("m2", "resv += 407")
+    cmd.alter("m2 & name O1P", "name = 'OP1'")
+    cmd.alter("m2 & name O2P", "name = 'OP2'")
+    cmd.alter("m2 & name O3P", "name = 'OP3'")
+    ccp4_ncont(f"{datadir}/2c7r.ncont", selName1="sel1", selName2="sel2")
+    assert cmd.count_atoms("sel1_res") == 23
+    assert cmd.count_atoms("sel1_atom") == 5
+    assert cmd.count_atoms("sel2_res") == 104
+    assert cmd.count_atoms("sel2_atom") == 16

scripts/flatten_obj.py

@@ -277,7 +277,7 @@ def flatten_obj(name="",selection="",state=0,rename=0,quiet=1,chain_map=""):
                 cmd.create(prefix, obj, state, 1)
 
         # renumber all states
-        statere = re.compile("^%s_(.*)_(\d+)$" % metaprefix) # matches split object names
+        statere = re.compile(r"^%s_(.*)_(\d+)$" % metaprefix) # matches split object names
 
         warn_lowercase = False
 
@@ -334,3 +334,25 @@ def flatten_obj(name="",selection="",state=0,rename=0,quiet=1,chain_map=""):
 # tab-completion of arguments
 cmd.auto_arg[0]['flatten_obj'] = [ cmd.object_sc, 'name or selection', '']
 cmd.auto_arg[1]['flatten_obj'] = [ cmd.object_sc, 'selection', '']
+
+
+def test_flatten_obj__rename0():
+    cmd.reinitialize()
+    cmd.fab("ACD", "m1", chain="C")
+    cmd.fab("DEF", "m2", chain="C")
+    flatten_obj("m3", "m1 | m2", rename=0)
+    assert cmd.count_atoms("m3") == 80
+    assert cmd.count_atoms("m3 & resi 2") == 26
+    assert cmd.get_chains("m3") == ["A", "C"]
+
+
+def test_flatten_obj__rename1():
+    cmd.reinitialize()
+    cmd.fab("ACD", "m1", chain="C")
+    cmd.fab("DEF", "m2", chain="C")
+    flatten_obj("m3", "m1 | m2", rename=1, chain_map="foo")
+    assert cmd.get_chains("m3") == ["A", "B"]
+    assert dict(stored.foo) == {
+        "A": ("m1", 1, "C"),
+        "B": ("m2", 1, "C"),
+    }

scripts/forster_distance_calculator.py

@@ -1,4 +1,4 @@
-'''
+r'''
 Described at PyMOL wiki:
 http://www.pymolwiki.org/index.php/forster_distance_calculator
 
@@ -77,7 +77,7 @@ def forster(D_Exi="ATTO488Exi.txt", D_Emi="ATTO488Emi.txt", A_Exi="ATTO590Exi.tx
     print("The .plt should be opened with gnuplot to make the graphs.")
     print("The created graphs are .eps files.")
     print("They can be converted to pdf with the program: epstopdf or eps2pdf")
-    print('Part of LaTeX: C:\Program Files (x86)\MiKTeX 2.9\miktex' + "\\" + "bin")
+    print(r'Part of LaTeX: C:\Program Files (x86)\MiKTeX 2.9\miktex' + "\\" + "bin")
     print("Or download here: http://tinyurl.com/eps2pdf")
 
     DonorEmi = open(D_Emi, "r")

scripts/plot_noe.py

@@ -56,10 +56,10 @@ def plot_noe(filename, line_color=None, line_width='1.0', advanced_coloring=0, s
     if advanced_coloring == 1:
         cmd.set("group_auto_mode", 2)
 
-    rgx_assi = re.compile("\s*[asignASIGN]+\s+.*")
-    rgx_or = re.compile("\s*[orOR]+\s+.*")
-    rgx_bracket = re.compile("(\(|\))")
-    rgx_tick = re.compile("(\w)\'")
+    rgx_assi = re.compile(r"\s*[asignASIGN]+\s+.*")
+    rgx_or = re.compile(r"\s*[orOR]+\s+.*")
+    rgx_bracket = re.compile(r"(\(|\))")
+    rgx_tick = re.compile(r"(\w)'")
 
     restraint_line = None
     restraint_block = []
@@ -68,17 +68,17 @@ def plot_noe(filename, line_color=None, line_width='1.0', advanced_coloring=0, s
     for line in open(filename):
         if rgx_assi.match(line):
             if restraint_line:
-                restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
+                restraint_block.append(rgx_tick.sub(r"\g<1>^", rgx_bracket.sub(" ", restraint_line)))
                 restraints_blocks.append(restraint_block)
             restraint_block = []
             restraint_line = line
         elif rgx_or.match(line):
-            restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
+            restraint_block.append(rgx_tick.sub(r"\g<1>^", rgx_bracket.sub(" ", restraint_line)))
             restraint_line = line
         else:
             restraint_line += line
 
-    restraint_block.append(rgx_tick.sub("\g<1>^", rgx_bracket.sub(" ", restraint_line)))
+    restraint_block.append(rgx_tick.sub(r"\g<1>^", rgx_bracket.sub(" ", restraint_line)))
     restraints_blocks.append(restraint_block)
 
     for restraint_block in restraints_blocks:

scripts/propka.py

@@ -1,4 +1,4 @@
-'''
+r'''
 Described at PyMOL wiki:
 http://www.pymolwiki.org/index.php/propka
 
@@ -222,7 +222,7 @@ def getpropka(PDB="NIL", chain="*", resi="0", resn="NIL", source="upload", PDBID
     assert version in ['v2.0', 'v3.0', 'v3.1'], "'version' has to be either: 'v2.0', 'v3.0', 'v3.1'"
     assert source in ['ID', 'upload', 'addr', 'input_file'], "'source' has to be either: 'ID', 'upload', 'addr', 'input_file'"
     if source == "upload":
-        assert PDB not in ['NIL'], "You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
+        assert PDB not in ['NIL'], r"You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
     if source == "ID":
         assert len(PDBID) == 4, "PDBID has to be 4 characters"
     # To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
@@ -517,7 +517,7 @@ def importpropkabonds(result_pka_pkafile):
 
 def createdirs():
     if platform.system() == 'Windows':
-        Newdir = os.getcwd() + "\Results_propka\\"
+        Newdir = os.getcwd() + "\\Results_propka\\"
     if platform.system() == 'Linux':
         Newdir = os.getcwd() + "/Results_propka/"
     if not os.path.exists(Newdir):

scripts/transformations.py

@@ -30,7 +30,7 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-"""Homogeneous Transformation Matrices and Quaternions.
+r"""Homogeneous Transformation Matrices and Quaternions.
 
 A library for calculating 4x4 matrices for translating, rotating, reflecting,
 scaling, shearing, projecting, orthogonalizing, and superimposing arrays of
@@ -883,7 +883,7 @@ def orthogonalization_matrix(lengths, angles):
 
 
 def affine_matrix_from_points(v0, v1, shear=True, scale=True, usesvd=True):
-    """Return affine transform matrix to register two point sets.
+    r"""Return affine transform matrix to register two point sets.
 
     v0 and v1 are shape (ndims, \*) arrays of at least ndims non-homogeneous
     coordinates, where ndims is the dimensionality of the coordinate space.
@@ -992,7 +992,7 @@ def affine_matrix_from_points(v0, v1, shear=True, scale=True, usesvd=True):
 
 
 def superimposition_matrix(v0, v1, scale=False, usesvd=True):
-    """Return matrix to transform given 3D point set into second point set.
+    r"""Return matrix to transform given 3D point set into second point set.
 
     v0 and v1 are shape (3, \*) or (4, \*) arrays of at least 3 points.
 

scripts/wfmesh.py

@@ -42,7 +42,7 @@ def readOBJ(self, file):
         if os.path.exists(file):
             input = open(file, 'r')
             for line in input:
-                dat = re.split("\s+", line)
+                dat = re.split(r"\s+", line)
 
                 # Find vertex line
                 if line[0] == 'v' and line[1] != 't' and line[1] != 'n':