test mmpa

Contrib/mmpa/README.md

@@ -0,0 +1,75 @@
+# MMPA
+
+## fragmentation
+```bash
+python rfrag.py < data/sample.smi > data/sample_fragmented.txt
+
+head -n 3 data/sample_fragmented.txt
+#
+# Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1,658387,Cc1cc([*:1])nn1[*:2],C[*:1].O=C(O)c1ccc(C[*:2])o1
+# Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1,658387,,C[*:1].Cc1cc([*:1])n(Cc2ccc(C(=O)O)o2)n1
+# format: WHOLE_MOL_SMILES,ID,SMILES_OF_CORE,SMILES_OF_CONTEXT
+```
+
+## indexing
+```bash
+python indexing.py < data/sample_fragmented.txt > data/sample_mmps_default.csv
+
+head -n 3 data/sample_mmps_default.csv
+# Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1,Cc1cc(C)n(Cc2ccc(C(=O)O)cc2)n1,658387,615212,c1cc([*:1])oc1C[*:2]>>c1cc([*:1])ccc1C[*:2],Cc1cc(C)n([*:2])n1.O=C(O)[*:1]
+# Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1,Cc1cc(C)n(Cc2ccc(C(=O)O)cc2)n1,658387,615212,c1cc([*:1])oc1[*:2]>>c1cc([*:1])ccc1[*:2],Cc1cc(C)n(C[*:1])n1.O=C(O)[*:2]
+# Cc1cc(C)n(Cc2ccc(C(=O)O)o2)n1,Cc1cc(C)n(Cc2ccc(C(=O)O)cc2)n1,658387,615212,O=C(O)c1ccc(C[*:1])o1>>O=C(O)c1ccc(C[*:1])cc1,Cc1cc(C)n([*:1])n1
+# format: SMILES_OF_LEFT_MMP,SMILES_OF_RIGHT_MMP,ID_OF_LEFT_MMP,ID_OF_RIGHT_MMP,SMIRKS_OF_TRANSFORMATION,SMILES_OF_CONTEXT
+```
+
+## create_db
+```bash
+python create_mmp_db.py -s < data/sample_fragmented.txt
+
+du -sh mmp.db
+# 56K     mmp.db
+```
+
+## search_db
+
+**Only support string match. it can't support smiles or smarts match.**
+
+### 1. mmp
+Find all MMPs of a input/query compound to the compounds in the db
+```bash
+cat data/sample_db_input_smi.txt
+# c1cc2c(ncnc2NCc2cccnc2)s1 2531831
+
+python search_mmp_db.py -t mmp < data/sample_db_input_smi.txt
+# c1cc2c(ncnc2NCc2cccnc2)s1,c1cc2c(ncnc2NCc2ccccc2)s1,2531831,2139597,c1ccc([*:1])cc1,c1nc(NC[*:1])c2ccsc2n1
+```
+
+### 2. subs
+Find all MMPs in the db where the LHS of the transform matches an input
+substructure.
+```bash
+cat data/sample_db_input_subs.txt
+# [*]c1ccccc1
+
+python search_mmp_db.py -t subs < data/sample_db_input_subs.txt
+# no result!
+```
+
+### 3. trans
+Find all MMPs that match the input transform/SMIRKS. Make sure the input SMIRKS has been canonicalised using the cansmirk.py program.
+
+```bash
+cat data/sample_db_input_trans.txt
+# [*:1]c1ccccc1>>[*:1]c1cccnc1,t1
+python search_mmp_db.py -t trans < data/sample_db_input_trans.txt
+# no result!
+
+tail -n 1 data/sample_mmps_default.csv
+# c1cc2c(ncnc2NCc2cccnc2)s1,c1cc2c(ncnc2NCc2ccccc2)s1,2531831,2139597,c1cncc([*:1])c1>>c1ccc([*:1])cc1,c1nc(NC[*:1])c2ccsc2n1
+
+echo 'c1cncc([*:1])c1>>c1ccc([*:1])cc1' > /tmp/trans.txt
+python search_mmp_db.py -t trans < /tmp/trans.txt
+# c1cc2c(ncnc2NCc2cccnc2)s1,c1cc2c(ncnc2NCc2ccccc2)s1,2531831,2139597,c1cncc([*:1])c1>>c1ccc([*:1])cc1,c1nc(NC[*:1])c2ccsc2n1
+
+```
+

Contrib/mmpa/create_mmp_db.py

@@ -241,6 +241,7 @@ def index_hydrogen_change():
 cursor.execute("CREATE INDEX core_smi_ni_idx ON core_table (core_smi_ni)")
 cursor.execute("DROP INDEX IF EXISTS smiles_idx")
 cursor.execute("CREATE INDEX smiles_idx ON cmpd_smisp (smiles)")
+con.commit()
 
 #add smarts searching capability if required
 if (options.sma):