Convert to python 3

.github/workflows/python-package.yml

@@ -0,0 +1,43 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10",]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Build and install with setuptools
+      run: |
+        python setup.py install
+    - name: Test with pytest
+      run: |
+        pytest example_scripts/

example_scripts/test_build.py

@@ -1,52 +1,52 @@
-from pmx import *
+from pmx import Molecule, Chain
+from pmx.builder import build_dna_strand
 
 
-# start a peptide chain from an amino acid
-mol = Molecule().new_aa( "ALA" )      # build alanine
-c = Chain( residues = [ mol ] )       # initialize chain
-c.nbuild("T")                         # extend at n-terminus
-c.cbuild("R")                         # extend at c-terminus
-c.write('TAR.pdb')                    # write pdb file
+def test_build():
+    # start a peptide chain from an amino acid
+    mol = Molecule().new_aa( "ALA" )      # build alanine
+    c = Chain( residues = [ mol ] )       # initialize chain
+    c.nbuild("T")                         # extend at n-terminus
+    c.cbuild("R")                         # extend at c-terminus
+    c.write('TAR.pdb')                    # write pdb file
 
-# build a peptide chain from sequence
+    # build a peptide chain from sequence
 
-sequence = "FRTLKNCWQ"
-c = Chain().create( sequence )
-c.write("extended.pdb")
+    sequence = "FRTLKNCWQ"
+    c = Chain().create( sequence )
+    c.write("extended.pdb")
 
-for resi in c.residues:
-    resi.set_phi( -57, True )
-    resi.set_psi( -47, True )
-c.write("helix_pep.pdb")
+    for resi in c.residues:
+        resi.set_phi( -57, True )
+        resi.set_psi( -47, True )
+    c.write("helix_pep.pdb")
 
-# fusing two chains
-seq = "LMNFRTS"
-c2 = Chain().create(seq)
-c.fuse( c2 )
-c.write("fused_pep.pdb")
+    # fusing two chains
+    seq = "LMNFRTS"
+    c2 = Chain().create(seq)
+    c.fuse( c2 )
+    c.write("fused_pep.pdb")
 
 
-# create repeating seuqences
+    # create repeating seuqences
 
 
 
-rep_seq = "HEATLLFT"
-c = Chain().create( rep_seq )  # start with new chain
-new_chain = c.copy()
+    rep_seq = "HEATLLFT"
+    c = Chain().create( rep_seq )  # start with new chain
+    new_chain = c.copy()
 
-for i in range(5):
-    c.fuse( new_chain.copy() )
-c.write("rep_pep.pdb")
-print c.sequence()
-helical_residues = c.fetch_residues(["HIS","GLU","ALA","THR","LEU"])
-for resi in helical_residues:
-    resi.set_phi( -57, True )
-    resi.set_psi( -47, True )
-c.write("repeat_helix.pdb")
+    for i in range(5):
+        c.fuse( new_chain.copy() )
+    c.write("rep_pep.pdb")
+    print(c.sequence())
+    helical_residues = c.fetch_residues(["HIS","GLU","ALA","THR","LEU"])
+    for resi in helical_residues:
+        resi.set_phi( -57, True )
+        resi.set_psi( -47, True )
+    c.write("repeat_helix.pdb")
 
 
-# building a DNA strand
-from pmx.builder import *
-model = build_dna_strand("ACGTGTCA")
-model.write("dna.pdb")
-
+    # building a DNA strand
+    model = build_dna_strand("ACGTGTCA")
+    model.write("dna.pdb")

example_scripts/test_edit.py

@@ -1,44 +1,45 @@
 import sys, os
-from pmx import *
+from pmx import Model, Chain
 
-seq1 = 'klrtsfcvnme'*2
-seq2 = 'irtiervcywq'*2
 
+def test_edit():
+    seq1 = 'klrtsfcvnme'*2
+    seq2 = 'irtiervcywq'*2
 
-c1 = Chain().create( seq1.upper() )
-c2 = Chain().create( seq2.upper() )
-c1.set_chain_id('A')
-c2.set_chain_id('B')
-c2.translate( [20,0,0] )
-m = Model(chains = [c1,c2] )
-m.write('protein.pdb')
 
-m = Model('protein.pdb')
+    c1 = Chain().create( seq1.upper() )
+    c2 = Chain().create( seq2.upper() )
+    c1.set_chain_id('A')
+    c2.set_chain_id('B')
+    c2.translate( [20,0,0] )
+    m = Model(chains = [c1,c2] )
+    m.write('protein.pdb')
 
-for atom in m.atoms:
-    print atom.id, atom.name, atom.resname
-
-for resi in m.residues:
-    if resi.resname in ['ALA','SER']:     # select some residues
-        print resi
-        for atom in resi.atoms:            
-            print atom.bfac                     # print some properties
+    m = Model('protein.pdb')
 
+    for atom in m.atoms:
+        print(atom.id, atom.name, atom.resname)
 
-for c in m.chains:
-    print c.id, len(c.residues), len(c.atoms) # print chain id, number of
-    # residues and number of atoms
+    for resi in m.residues:
+        if resi.resname in ['ALA','SER']:     # select some residues
+            print(resi)
+            for atom in resi.atoms:
+                print(atom.bfac)                     # print some properties
 
-chainB = m.chdic['B']            # select chain
-for atom in chainB.atoms:
-    print atom.occ
 
+    for c in m.chains:
+        print(c.id, len(c.residues), len(c.atoms)) # print chain id, number of
+        # residues and number of atoms
 
-resl = m.fetch_residues(["LEU","PHE"])
-for r in resl:
-    print 'leu_or_phe:', r
+    chainB = m.chdic['B']            # select chain
+    for atom in chainB.atoms:
+        print(atom.occ)
 
-resl = m.fetch_residues(["LEU","PHE"], inv = True)
-for r in resl:
-    print 'not leu_or_phe:', r
 
+    resl = m.fetch_residues(["LEU","PHE"])
+    for r in resl:
+        print('leu_or_phe:', r)
+
+    resl = m.fetch_residues(["LEU","PHE"], inv = True)
+    for r in resl:
+        print('not leu_or_phe:', r)

example_scripts/test_ffparser.py

@@ -1,37 +1,38 @@
 import sys, os
 
-from pmx.forcefield2 import *
+from pmx.forcefield2 import ITPFile
 
-top = ITPFile( sys.argv[1])
-## for atom in top.atoms:
-##     atom.atomtypeB = 'DUM'
-##     atom.qB = 0
-##     atom.mB = atom.m
-top.write('new.itp')
 
+def test_ffparser():
+    top = ITPFile('./protLig_benchmark/pde2/ligands_cgenff/lig_50181001/MOL.itp')
+    ## for atom in top.atoms:
+    ##     atom.atomtypeB = 'DUM'
+    ##     atom.qB = 0
+    ##     atom.mB = atom.m
+    top.write('new.itp')
 
-## from pmx.ffparser import *
-## ## from pmx.library import _aacids_dic
-## rtp = RTPParser( 'ffamber99sb.rtp')
-## print rtp['ALA']
 
-## for name, entry in rtp:
-##     print name, entry['atoms'][0]
-## print 'XXX'
-## for name, entry in rtp:
-##     print name, entry['atoms'][0]
-## ala = rtp['ALA']
-## print _aacids_dic
-## for aa in _aacids_dic.values():
-##     try:
-##         del rtp[aa]
-##     except:
-##         pass
-## rtp.add_entry( "ala", ala )
-## print "ala" in rtp
-#rtp.write(sys.stdout)
-#print rtp["ALA"]['bonds']
+    ## from pmx.ffparser import *
+    ## ## from pmx.library import _aacids_dic
+    ## rtp = RTPParser( 'ffamber99sb.rtp')
+    ## print rtp['ALA']
 
-#nb = NBParser("ffamber99sbnb.itp")
-#print nb
+    ## for name, entry in rtp:
+    ##     print name, entry['atoms'][0]
+    ## print 'XXX'
+    ## for name, entry in rtp:
+    ##     print name, entry['atoms'][0]
+    ## ala = rtp['ALA']
+    ## print _aacids_dic
+    ## for aa in _aacids_dic.values():
+    ##     try:
+    ##         del rtp[aa]
+    ##     except:
+    ##         pass
+    ## rtp.add_entry( "ala", ala )
+    ## print "ala" in rtp
+    #rtp.write(sys.stdout)
+    #print rtp["ALA"]['bonds']
 
+    #nb = NBParser("ffamber99sbnb.itp")
+    #print nb

example_scripts/test_index.py

@@ -2,12 +2,16 @@
 from pmx import *
 from pmx.ndx import *
 
-m = Model( "gmx.pdb" )
+m = Model( "./protLig_benchmark/cdk2/ligands_gaff2/lig_1h1q/mol_gmx.pdb" )
+
+import pytest
+pytest.skip(allow_module_level=True)
+# skip because don't have an example .ndx file
 
 ndx = IndexFile("index.ndx")
 
-print ndx
-print ndx['Backbone']
+print(ndx)
+print(ndx['Backbone'])
 
 atoms = ndx['Backbone'].select_atoms( m )
 del ndx['Backbone']
@@ -17,7 +21,6 @@
 
 
 
-print ndx
+print(ndx)
 #for atom in atoms:
 #    print atom
-

example_scripts/test_insert.py

@@ -1,18 +1,17 @@
 import sys, os
-from pmx import *
+from pmx import Model, Chain
 
-## c = Chain().create("ALKIRTS")
+def test_insert():
+    c = Chain().create("ALKIRTS")
+    m = Model("./protLig_benchmark/cdk2/protein_amber/protein.pdb")
 
-## m = Model("protein.pdb")
-
-## chB = m.chdic["B"]
-
-## chB.insert_chain(2, c )
-## m.write("ins.pdb")
-c = Chain().create("ALT")   
-print c.atoms[0].name
-del c.atoms[0]                    # delete list item, first atom is gone
-print c.atoms[0].name                  # first atom is a different one now
-atom = c.residues[0].atoms[0]     # select first atom from the first residue
-print atom.name                        # should be the same as above
+    chB = m.chdic["B"]
+    chB.insert_chain(2, c )
+    m.write("ins.pdb")
 
+    c = Chain().create("ALT")
+    print(c.atoms[0].name)
+    del c.atoms[0]                    # delete list item, first atom is gone
+    print(c.atoms[0].name)                  # first atom is a different one now
+    atom = c.residues[0].atoms[0]     # select first atom from the first residue
+    print(atom.name)                        # should be the same as above

example_scripts/test_new_rot.py

@@ -6,4 +6,3 @@
     r.set_phi( -57, True )
     r.set_psi( -47, True )
 c.write('hel.pdb')
-

example_scripts/test_opt.py

@@ -1,3 +1,6 @@
+import pytest
+pytest.skip(allow_module_level=True)
+
 import sys, os
 from pmx import *
 
@@ -13,21 +16,19 @@
 
 
 file_options = [
-    FileOption("-pdb", "r",["pdb"], "protein.pdb", "input pdb file"), 
-    FileOption("-opdb", "w",["pdb","gro"], "out.pdb", "output pdb or gro file"),  
-    FileOption("-mpdb", "r/m",["pdb","gro"], "one_of_many.pdb", "several pdb files"),  
+    FileOption("-pdb", "r",["pdb"], "protein.pdb", "input pdb file"),
+    FileOption("-opdb", "w",["pdb","gro"], "out.pdb", "output pdb or gro file"),
+    FileOption("-mpdb", "r/m",["pdb","gro"], "one_of_many.pdb", "several pdb files"),
     ]
 
 help_text = [ "This program does useful things",
               "as long as you use option a,b and c",
               "but not in combination with d and e"]
 
 
-cmdl = Commandline( sys.argv, options = options, fileoptions = file_options, program_desc = help_text, version = "2.3") 
-
-
+cmdl = Commandline( sys.argv, options = options, fileoptions = file_options, program_desc = help_text, version = "2.3")
 
-string_opt = cmdl['-s'] 
-input_pdb = cmdl['-pdb'] 
 
 
+string_opt = cmdl['-s']
+input_pdb = cmdl['-pdb']