basic idea for templates to create permutations of possible donor / acceptor H sites

.pre-commit-config.yaml

@@ -17,14 +17,14 @@ repos:
     -   id: trailing-whitespace
         types: [python]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.10.1
     hooks:
     -   id: pyupgrade
         args:
         - --py39-plus
         - --keep-runtime-typing
--   repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.287
     hooks:
     -   id: ruff
         verbose: True

README.md

@@ -5,7 +5,7 @@ protex
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protex/forcefield/toh2/toppar/cl_d.str

@@ -0,0 +1,42 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Marta from protein master 2013
+
+RESI CLA          -1.000 ! Chloride Ion 
+GROUP 
+ATOM CLA  CLAD    -1.000  ALPHA -3.969 TYPE DPPOL 
+PATCHING FIRST NONE LAST NONE 
+
+END
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+
+ANGLES
+
+DIHEDRALS
+
+IMPROPERS
+
+
+END
+RETURN

protex/forcefield/toh2/toppar/h2o_d.str

@@ -0,0 +1,62 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Converts cgenff atomtype to drude atom types.
+! Charges are picked from cgenff stream file
+! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
+! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.
+
+RESI H2O          0.000 ! 
+GROUP 
+ATOM OH2  OPOL13     -0.669   ALPHA -1.44 THOLE 1.3 
+ATOM H1   HPOL      0.3345 
+ATOM H2   HPOL      0.3345
+ATOM H3   DUMH     0.000
+ATOM H4   DUMH     0.000
+BOND OH2 H1 
+BOND OH2 H2 
+BOND OH2 H3
+BOND OH2 H4 
+!ANGLE  H1 OH2 H2
+!ANGLE  H1 OH2 H3
+!ANGLE  H3 OH2 H2
+!ANGLE  H1 OH2 H4
+!ANGLE  H2 OH2 H4
+!ANGLE  H3 OH2 H4
+
+
+!PATCH FIRST NONE LAST NONE 
+
+END
+
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+
+ANGLES
+
+DIHEDRALS
+
+IMPROPERS
+
+
+END
+RETURN

protex/forcefield/toh2/toppar/h3o_d.str

@@ -0,0 +1,62 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Converts cgenff atomtype to drude atom types.
+! Charges are picked from cgenff stream file
+! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
+! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.
+
+!TETRA-WATER by Max
+RESI H3O           1.0000
+GROUP 
+ATOM OH2  OPOL13   -0.4871  ALPHA -1.09 TYPE DPPOL THOLE 1.3     
+ATOM H1   HPOL      0.4957 
+ATOM H2   HPOL      0.4957 
+ATOM H3   HPOL      0.4957 
+ATOM H4   DUMH      0.0000
+BOND OH2 H1 
+BOND OH2 H2 
+BOND OH2 H3
+BOND OH2 H4 
+!ANGLE  H1 OH2 H2
+!ANGLE  H1 OH2 H3
+!ANGLE  H3 OH2 H2
+!ANGLE  H1 OH2 H4
+!ANGLE  H2 OH2 H4
+!ANGLE  H3 OH2 H4
+
+!PATCH FIRST NONE LAST NONE 
+
+END
+
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+
+ANGLES
+
+DIHEDRALS
+
+IMPROPERS
+
+
+END
+RETURN

protex/forcefield/toh2/toppar/na_d.str

@@ -0,0 +1,42 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Marta from protein master 2013
+
+RESI SOD           1.000 ! Sodium Ion 
+GROUP 
+ATOM SOD  SODD     1.000  ALPHA -0.157 
+PATCHING FIRST NONE LAST NONE 
+
+END
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+
+ANGLES
+
+DIHEDRALS
+
+IMPROPERS
+
+
+END
+RETURN

protex/forcefield/toh2/toppar/oh_d.str

@@ -0,0 +1,59 @@
+* Toppar stream file generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+ioformat extended
+
+read rtf card append
+* Topologies generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+44
+
+AUTO ANGL DIHE DRUD
+
+! Converts cgenff atomtype to drude atom types.
+! Charges are picked from cgenff stream file
+! Alpha and Thole values are picked from first match of atom type in a text file containing all currently available residues.
+! If it cannot find the values -1.0 and -1.3 values are assigned to the atom type.
+
+RESI OH     -1.0000
+GROUP
+ATOM OH2   OPOL13          -1.320   ALPHA   -1.0000 TYPE DPPOL  THOLE   1.3000 ! ODW and HDW atom types from SWM4 water, Marta
+ATOM H1   HPOL          0.320 
+ATOM H2   DUMH          0.000 
+ATOM H3   DUMH     0.000
+ATOM H4   DUMH     0.000
+BOND OH2 H1 
+BOND OH2 H2 
+BOND OH2 H3
+BOND OH2 H4 
+!ANGLE  H1 OH2 H2
+!ANGLE  H1 OH2 H3
+!ANGLE  H3 OH2 H2
+!ANGLE  H1 OH2 H4
+!ANGLE  H2 OH2 H4
+!ANGLE  H3 OH2 H4
+
+END
+
+
+read param card append
+* Parameters generated by FFParam cgenfftoconverter
+* For use with Drude force field
+*
+
+! Parameters are picked from same text file containing all currently available parameters.
+! Similar approach like cgenff is applied, but it is not checked for its robustness.
+
+BONDS
+
+ANGLES
+
+DIHEDRALS
+
+IMPROPERS
+
+
+END
+RETURN