medchem_fragment_splitter: changeset 4:5da3079a3008

--- a/Readme.md	Tue Sep 06 10:51:09 2022 +0300
+++ b/Readme.md	Tue Sep 06 23:59:06 2022 +0300
@@ -3,10 +3,35 @@
 Split a drug like molecule into fragments meaningful from the viewpoint of Medicinal Chemistry.
 
 **Descriptopn**
-TODO: insert
+The following options are available in script:
+-l - path to ligand file;
+-w - path to working directory;
+-s - path to file with SMARTS expression;
+-p - no parameter, option if needed a picture;
+-x - no parameter, option if needed to save fragment-files
+-a - no parameter, option if needed to be decomposed by inner rules
+
+The application can work in several modes. The first mode decomposes molecules by the built-in set of SMARTS-expressions. It is achieved using parameter ‘-s’ and a file with defined SMARTS-expressions:
+
+>./defragmentation.py -l ..path-to-ligand -w ..path-to-work-directory -s ..SMARTS-expressions -x -p
+
+What is more, these expressions must describe non-overlaid fragments. The second mode lets to decompose molecules by the rules described in current article. It is achieved using parameter ‘-a’:
+
+>./defragmentation.py -l ..path-to-ligand -w ..path-to-work-directory -x -p -a
+
+The parameter ‘-x’ is used to write files of fragments:
+
+>./defragmentation.py -l ..path-to-ligand -w ..path-to-work-directory -x -a
+
+The parameter ‘-p’ is used to generate a picture of a molecule's structure with colored fragments:
+
+>./defragmentation.py -l ..path-to-ligand -w ..path-to-work-directory -p -a
+
+To produce the output at least one parameter ‘-x’ or ‘-p’ should be used.
 
 **Installation and requirements**
-TODO: insert
+- Python3
+- RDKit version 2020.03 or later
 
 **Examples of application**
 TODO: insert

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/DB00176.smi	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,1 @@
+COCCCC\C(=N/OCCN)C1=CC=C(C=C1)C(F)(F)F
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/DB08865.smi	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,1 @@
+[H][C@](C)(OC1=CC(=CN=C1N)C1=CN(N=C1)C1CCNCC1)C1=C(Cl)C=CC(F)=C1Cl
\ No newline at end of file

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+++ b/files/output_DB00176.smi.svg	Tue Sep 06 23:59:06 2022 +0300
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+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_1_C2H4.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,9 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    4  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    5  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    6  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    3
+CONECT    2    4    5    6
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_1_CH4O.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,9 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
+HETATM    3  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    4  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    5  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    6  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    3    4    5
+CONECT    2    6
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_2_C4H10.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,19 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3  C3  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    4  C4  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    5  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    6  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    7  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    8  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    9  H5  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   10  H6  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   11  H7  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   12  H8  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   13  H9  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   14  H10 UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    5    6    7
+CONECT    2    3    8    9
+CONECT    3    4   10   11
+CONECT    4   12   13   14
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_2_C8H8N4O.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,35 @@
+HETATM    1  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
+HETATM    2  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    4  C3  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    5  C4  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    6  N1  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM    7  C5  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    8  N2  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM    9  C6  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM   10  C7  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM   11  N3  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM   12  N4  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM   13  C8  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM   14  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   15  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   16  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   17  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   18  H5  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   19  H6  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   20  H7  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   21  H8  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2   14
+CONECT    2    3    3    7
+CONECT    3    4   15
+CONECT    4    5    5    9
+CONECT    5    6   16
+CONECT    6    7    7
+CONECT    7    8
+CONECT    8   17   18
+CONECT    9   10   10   13
+CONECT   10   11   19
+CONECT   11   12   20
+CONECT   12   13   13
+CONECT   13   21
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_3_C5H11N.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,24 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3  C3  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    4  N1  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM    5  C4  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    6  C5  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    7  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    8  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    9  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   10  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   11  H5  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   12  H6  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   13  H7  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   14  H8  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   15  H9  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   16  H10 UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   17  H11 UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    6    7    8
+CONECT    2    3    9   10
+CONECT    3    4   11   12
+CONECT    4    5   13
+CONECT    5    6   14   15
+CONECT    6   16   17
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_3_C7H7NO.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,26 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  N1  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM    3  O1  UNL     1       0.000   0.000   0.000  1.00  0.00           O  
+HETATM    4  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    5  C3  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    6  C4  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    7  C5  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    8  C6  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    9  C7  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM   10  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   11  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   12  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   13  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   14  H5  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   15  H6  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   16  H7  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    2    4   10
+CONECT    2    3
+CONECT    3   11
+CONECT    4    5    5    9
+CONECT    5    6   12
+CONECT    6    7    7   13
+CONECT    7    8   14
+CONECT    8    9    9   15
+CONECT    9   16
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_4_C2H7N.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,14 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3  N1  UNL     1       0.000   0.000   0.000  1.00  0.00           N  
+HETATM    4  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    5  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    6  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    7  H4  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    8  H5  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM    9  H6  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   10  H7  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    4    5    6
+CONECT    2    3    7    8
+CONECT    3    9   10
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_4_C6H3Cl2F.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,19 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    3 CL1  UNL     1       0.000   0.000   0.000  1.00  0.00          CL  
+HETATM    4  C3  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    5  C4  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    6  C5  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    7  F1  UNL     1       0.000   0.000   0.000  1.00  0.00           F  
+HETATM    8  C6  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    9 CL2  UNL     1       0.000   0.000   0.000  1.00  0.00          CL  
+HETATM   10  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   11  H2  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+HETATM   12  H3  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    2    8   10
+CONECT    2    3    4
+CONECT    4    5    5   11
+CONECT    5    6   12
+CONECT    6    7    8    8
+CONECT    8    9
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/output_ligand_5_CHF3.pdb	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,7 @@
+HETATM    1  C1  UNL     1       0.000   0.000   0.000  1.00  0.00           C  
+HETATM    2  F1  UNL     1       0.000   0.000   0.000  1.00  0.00           F  
+HETATM    3  F2  UNL     1       0.000   0.000   0.000  1.00  0.00           F  
+HETATM    4  F3  UNL     1       0.000   0.000   0.000  1.00  0.00           F  
+HETATM    5  H1  UNL     1       0.000   0.000   0.000  1.00  0.00           H  
+CONECT    1    2    3    4    5
+END

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/files/test.sh	Tue Sep 06 23:59:06 2022 +0300
@@ -0,0 +1,81 @@
+#!/bin/bash
+
+python ../medchem_fragment_splitter.py -l DB08865.smi -w . -p -x -a
+SVG_DB08865=$(diff DB08865.smi.svg output_DB08865.smi.svg | wc -c)
+if [[ ${SVG_DB08865} -eq '0' ]]; then
+	echo "Draw SVG Test 1 OK!"
+else
+	echo "Draw SVG Test 1 Error!"
+fi
+PNG_DB08865=$(diff -s DB08865.smi.png output_DB08865.smi.png)
+if [[ $PNG_DB08865 == *"identical" ]]; then
+	echo "Draw PNG Test 2 OK!"
+else
+	echo "Draw PNG Test 2 Error!"
+fi
+
+PDB_1_LIGAND=$(diff ligand_1_C2H4.pdb output_ligand_1_C2H4.pdb | wc -c)
+PDB_2_LIGAND=$(diff ligand_2_C8H8N4O.pdb output_ligand_2_C8H8N4O.pdb | wc -c)
+PDB_3_LIGAND=$(diff ligand_3_C5H11N.pdb output_ligand_3_C5H11N.pdb | wc -c)
+PDB_4_LIGAND=$(diff ligand_4_C6H3Cl2F.pdb output_ligand_4_C6H3Cl2F.pdb | wc -c)
+PDB_SUM=0
+((PDB_SUM+=PDB_1_LIGAND))
+((PDB_SUM+=PDB_2_LIGAND))
+((PDB_SUM+=PDB_3_LIGAND))
+((PDB_SUM+=PDB_4_LIGAND))
+
+if [[ ${PDB_SUM} -eq '0' ]]; then
+	echo "Decomposition Test 3 OK!"
+else
+	echo "Decomposition Test 3 Error!"
+fi
+
+# clean up
+rm DB08865.smi.svg
+rm DB08865.smi.png
+rm ligand_1_C2H4.pdb
+rm ligand_2_C8H8N4O.pdb
+rm ligand_3_C5H11N.pdb
+rm ligand_4_C6H3Cl2F.pdb
+
+# Test 4-6
+python ../medchem_fragment_splitter.py -l DB00176.smi -w . -p -x -a
+SVG_DB00176=$(diff DB00176.smi.svg output_DB00176.smi.svg | wc -c)
+if [[ ${SVG_DB00176} -eq '0' ]]; then
+	echo "Draw SVG Test 4 OK!"
+else
+	echo "Draw SVG Test 4 Error!"
+fi
+PNG_DB00176=$(diff -s DB00176.smi.png output_DB00176.smi.png)
+if [[ $PNG_DB00176 == *"identical" ]]; then
+	echo "Draw PNG Test 5 OK!"
+else
+	echo "Draw PNG Test 5 Error!"
+fi
+
+PDB_1_LIGAND=$(diff ligand_1_CH4O.pdb output_ligand_1_CH4O.pdb | wc -c)
+PDB_2_LIGAND=$(diff ligand_2_C4H10.pdb output_ligand_2_C4H10.pdb | wc -c)
+PDB_3_LIGAND=$(diff ligand_3_C7H7NO.pdb output_ligand_3_C7H7NO.pdb | wc -c)
+PDB_4_LIGAND=$(diff ligand_4_C2H7N.pdb output_ligand_4_C2H7N.pdb | wc -c)
+PDB_5_LIGAND=$(diff ligand_5_CHF3.pdb output_ligand_5_CHF3.pdb | wc -c)
+PDB_SUM=0
+((PDB_SUM+=PDB_1_LIGAND))
+((PDB_SUM+=PDB_2_LIGAND))
+((PDB_SUM+=PDB_3_LIGAND))
+((PDB_SUM+=PDB_4_LIGAND))
+((PDB_SUM+=PDB_5_LIGAND))
+
+if [[ ${PDB_SUM} -eq '0' ]]; then
+	echo "Decomposition Test 6 OK!"
+else
+	echo "Decomposition Test 6 Error!"
+fi
+
+# clean up
+rm DB00176.smi.svg
+rm DB00176.smi.png
+rm ligand_1_CH4O.pdb
+rm ligand_2_C4H10.pdb
+rm ligand_3_C7H7NO.pdb
+rm ligand_4_C2H7N.pdb
+rm ligand_5_CHF3.pdb
\ No newline at end of file

author	Nikita Ivanov <n4knikita@qsar.chem.msu.ru>
	Tue, 06 Sep 2022 23:59:06 +0300
branch	develop
changeset 4	5da3079a3008
parent 3	69ed2556e933
child 5	fbc02d3d34ca

Readme.md		file \| annotate \| diff \| comparison \| revisions
files/DB00176.smi		file \| annotate \| diff \| comparison \| revisions
files/DB08865.smi		file \| annotate \| diff \| comparison \| revisions
files/output_DB00176.smi.png		file \| annotate \| diff \| comparison \| revisions
files/output_DB00176.smi.svg		file \| annotate \| diff \| comparison \| revisions
files/output_DB08865.smi.png		file \| annotate \| diff \| comparison \| revisions
files/output_DB08865.smi.svg		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_1_C2H4.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_1_CH4O.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_2_C4H10.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_2_C8H8N4O.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_3_C5H11N.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_3_C7H7NO.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_4_C2H7N.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_4_C6H3Cl2F.pdb		file \| annotate \| diff \| comparison \| revisions
files/output_ligand_5_CHF3.pdb		file \| annotate \| diff \| comparison \| revisions
files/test.sh		file \| annotate \| diff \| comparison \| revisions