From 352a22b7b85de156fe0f1b0560d43fe4fa72913f Mon Sep 17 00:00:00 2001
From: JohannesKarwou <johannes.karwou@gmail.com>
Date: Mon, 1 Aug 2022 15:38:01 +0200
Subject: [PATCH] giving the option of readint in str files

---
 transformato/charmm_factory.py | 20 +++++++++++++++++++-
 transformato/state.py          | 27 ++++++++++++++++++++++++---
 transformato/system.py         |  3 ++-
 3 files changed, 45 insertions(+), 5 deletions(-)

diff --git a/transformato/charmm_factory.py b/transformato/charmm_factory.py
index 44e66a9b..d6760224 100644
--- a/transformato/charmm_factory.py
+++ b/transformato/charmm_factory.py
@@ -1,6 +1,7 @@
 import datetime
 from transformato.constants import temperature, charmm_gpu
 from openmm import unit
+import os
 
 
 class CharmmFactory:
@@ -65,7 +66,7 @@ def generate_CHARMM_production_files(self, env: str) -> str:
         return charmm_production_script
 
     @staticmethod
-    def build_reduced_toppar(tlc: str) -> str:
+    def build_reduced_toppar(tlc: str, charmm_gui_base :str) -> str:
         date = datetime.date.today()
         toppar = f"""* Simplified toppar script
 * Version from {date}
@@ -168,8 +169,11 @@ def build_reduced_toppar(tlc: str) -> str:
 ! Additional topologies and parameters for spin/fluorophore labels
 stream ../../toppar/toppar_all36_label_spin.str
 stream ../../toppar/toppar_all36_label_fluorophore.str
+"""
 
 
+        if os.path.isfile(f"{charmm_gui_base}/waterbox/{tlc.lower()}/{tlc.lower()}_g.rtf"):
+            toppar += f"""
 ! Read {tlc} RTF
 open read unit 10 card name {tlc}_g.rtf
 read rtf card unit 10 append
@@ -185,8 +189,22 @@ def build_reduced_toppar(tlc: str) -> str:
 ! Read dummy_atom prm
 open read unit 10 card name dummy_parameters.prm
 read para card unit 10 append flex
+"""
+        else:
+            toppar += f"""
+! Read {tlc} STR
+stream {tlc}.str
+read para card unit 10 append flex
+
+! Read dummy_atom RTF
+open read unit 10 card name dummy_atom_definitions.rtf
+read rtf card unit 10 append
 
+! Read dummy_atom prm
+open read unit 10 card name dummy_parameters.prm
+read para card unit 10 append flex
 """
+
         return toppar
 
     def _get_CHARMM_production_header(self, env: str) -> str:
diff --git a/transformato/state.py b/transformato/state.py
index 990bd3d2..12ced72c 100644
--- a/transformato/state.py
+++ b/transformato/state.py
@@ -515,6 +515,15 @@ def _copy_ligand_specific_top_and_par(
         toppar_target = f"{intermediate_state_file_path}/{self.system.tlc.lower()}.prm"
         shutil.copyfile(ligand_prm, toppar_target)
 
+    def _copy_ligand_specific_str(
+        self, basedir: str, intermediate_state_file_path: str
+    ):
+
+        # copy ligand rtf file
+        ligand_rtf = f"{basedir}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}.str"
+        toppar_target = (f"{intermediate_state_file_path}/{self.system.tlc.lower()}.str")
+        shutil.copyfile(ligand_rtf, toppar_target)
+
     def _copy_crd_file(self, intermediate_state_file_path: str):
 
         basedir = self.system.charmm_gui_base
@@ -538,7 +547,12 @@ def _copy_files(self, intermediate_state_file_path: str):
 
         basedir = self.system.charmm_gui_base
 
-        self._copy_ligand_specific_top_and_par(basedir, intermediate_state_file_path)
+        try:
+            self._copy_ligand_specific_top_and_par(basedir, intermediate_state_file_path)
+        except:
+            self._copy_ligand_specific_str(basedir, intermediate_state_file_path)
+
+
 
         # copy crd file
         self._copy_crd_file((intermediate_state_file_path))
@@ -964,10 +978,17 @@ def _write_toppar_str(self, output_file_base):
 ../../toppar/toppar_all36_lipid_model.str
 ../../toppar/toppar_all36_lipid_prot.str
 ../../toppar/toppar_all36_lipid_sphingo.str
-{self.system.tlc.lower()}_g.rtf
+"""
+        if os.path.isfile(f"{self.system.charmm_gui_base}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}_g.rtf"):
+            toppar_format += f"""{self.system.tlc.lower()}_g.rtf
 {self.system.tlc.lower()}.prm
 dummy_atom_definitions.rtf
 dummy_parameters.prm
+"""
+        else:
+            toppar_format += f"""{self.system.tlc.lower()}.str
+dummy_atom_definitions.rtf
+dummy_parameters.prm
 """
 
         f = open(f"{output_file_base}/toppar.str", "w+")
@@ -976,7 +997,7 @@ def _write_toppar_str(self, output_file_base):
 
         # write charmm_toppar.str
         charmm_toppar = self.charmm_factory.build_reduced_toppar(
-            self.system.tlc.lower()
+            self.system.tlc.lower(), self.system.charmm_gui_base
         )
 
         f = open(f"{output_file_base}/charmm_toppar.str", "w+")
diff --git a/transformato/system.py b/transformato/system.py
index a42549b5..a5ff0b7e 100644
--- a/transformato/system.py
+++ b/transformato/system.py
@@ -168,8 +168,9 @@ def _read_parameters(self, env: str) -> pm.charmm.CharmmParameterSet:
         parameter_files = tuple()
         l1 = f"{charmm_gui_env}/{tlc_lower}/{tlc_lower}.rtf"
         l2 = f"{charmm_gui_env}/{tlc_lower}/{tlc_lower}.prm"
+        l3 = f"{charmm_gui_env}/{tlc_lower}/{tlc_lower}.str"
 
-        for file_path in [l1, l2]:
+        for file_path in [l1, l2, l3]:
             if os.path.isfile(file_path):
                 parameter_files += (file_path,)
             else: