Open selcenari opened 3 years ago
In the first case you have a PO3H vs PO3- in the second. It can't use that H if it didn't exist....
Also when you say completely different, the input order of the atoms can determine the orientation of the structures when drawn from SMILES. In that case then yes canonicalising first would help but in this case it looks like there were different inputs so the canonical SMILES would still be different. Also note that mapping numbers mean nothing, it's the relationship between them that matters.
For example:
[CH3:3][CH2:2].[OH:1]>>[CH3:3][CH2:2][OH:1]
[OH:1].[CH3:3][CH2:2]>>[CH3:3][CH2:2][OH:1]
mean the same thing but you may get different colors.
In this case, they may not have given the SMILES that have been used for mapping on their web page or datasets. I see what you mean about mapping numbers. It was very helpful.
Thank you so much!!! 👍
Likely the SMILES is normalised to physiological pH, e.g. -CO2H => -CO2–
I understand. So, do you suggest a tool that can normalize reaction smiles as in physiological conditions or a database that offers normalized rxn files?
Hi,
I am trying to map atoms of molecules supported by Recon 3D. In Recon 3D study Reaction Decoder tool have been also used, and the mapped reactions can be found in Virtual Metabolic Human.
Here is my problem. When i performed AAM in the same reactions by using SMILES of metabolites which are obtained from VHM, i can not obtained the same mapping images.
As an example: DHCR72r reaction in cholestrol metabolism
When it was searched DHCR72r reaction in VMH, following image are found:
Reaction is given as 7dhchsterol[r] + h[r] + nadph[r] -> chsterol[r] + nadp[r]
Metabolites are
products:
chsterol: [H]O[C@]1([H])C([H])([H])C2=C([H])C([H])([H])[C@@]3([H])[C@]4([H])C([H])([H])C([H])([H])C@(C@(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H] nadp: [H]O[C@]1([H])C@(O[H])C@(O[C@@]1([H])[N+]1=C([H])C(=C([H])C([H])=C1[H])C(=O)N([H])[H])C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]1([H])OC@@(N2C([H])=NC3=C(N=C([H])N=C23)N([H])[H])C@(OP([O-])([O-])=O)[C@]1([H])O[H]
rxn: [H]O[C@]1([H])C([H])([H])C2=C([H])C([H])=C3[C@]4([H])C([H])([H])C([H])([H])C@(C@(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H].[H+].[H]O[C@@]1([H])C@@(OC@(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])OC@@(N3C([H])=NC4=C(N=C([H])N=C34)N([H])[H])C@(OP([O-])([O-])=O)[C@]2([H])O[H])[C@@]1([H])O[H])N1C([H])=C([H])C([H])([H])C(=C1[H])C(=O)N([H])[H]>>[H]O[C@]1([H])C([H])([H])C2=C([H])C([H])([H])[C@@]3([H])[C@]4([H])C([H])([H])C([H])([H])C@(C@(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H].[H]O[C@]1([H])C@(O[H])C@(O[C@@]1([H])[N+]1=C([H])C(=C([H])C([H])=C1[H])C(=O)N([H])[H])C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]1([H])OC@@(N2C([H])=NC3=C(N=C([H])N=C23)N([H])[H])C@(OP([O-])([O-])=O)[C@]1([H])O[H]
java -jar rdt-2.4.1-jar-with-dependencies.jar -Q SMI -q '[H]O[C@]1([H])C([H])([H])C2=C([H])C([H])=C3[C@]4([H])C([H])([H])C([H])([H])C@(C@(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H].[H+].[H]O[C@@]1([H])C@@(OC@(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])OC@@(N3C([H])=NC4=C(N=C([H])N=C34)N([H])[H])C@(OP([O-])([O-])=O)[C@]2([H])O[H])[C@@]1([H])O[H])N1C([H])=C([H])C([H])([H])C(=C1[H])C(=O)N([H])[H]>>[H]O[C@]1([H])C([H])([H])C2=C([H])C([H])([H])[C@@]3([H])[C@]4([H])C([H])([H])C([H])([H])C@(C@(C([H])([H])[H])C([H])([H])C([H])([H])C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@@]4(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])[C@@]2(C([H])([H])[H])C([H])([H])C1([H])[H].[H]O[C@]1([H])C@(O[H])C@(O[C@@]1([H])[N+]1=C([H])C(=C([H])C([H])=C1[H])C(=O)N([H])[H])C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]1([H])OC@@(N2C([H])=NC3=C(N=C([H])N=C23)N([H])[H])C@(OP([O-])([O-])=O)[C@]1([H])O[H]' -c -g -j AAM -p tests/ -f TEXT
0 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading global configuration 5 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading defaults: jar:file:/truba/home/sariyuka/reaction-decoder/rdt-2.4.1-jar-with-dependencies.jar!/META-INF/jnati/jnati.default-properties 6 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact configuration: jniinchi-1.03_1 7 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults: jar:file:/truba/home/sariyuka/reaction-decoder/rdt-2.4.1-jar-with-dependencies.jar!/META-INF/jnati/jnati.instance.default-properties 10 [main] INFO net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath for: jniinchi-1.03_1-LINUX-AMD64 12 [main] INFO net.sf.jnati.deploy.repository.LocalRepository - Searching local repository for: jniinchi-1.03_1-LINUX-AMD64 12 [main] DEBUG net.sf.jnati.deploy.repository.LocalRepository - Artefact path: /truba/home/sariyuka/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 26 [main] INFO net.sf.jnati.deploy.artefact.ManifestReader - Reading manifest 90 [main] INFO net.sf.jnati.deploy.NativeArtefactLocator - Artefact (jniinchi-1.03_1-LINUX-AMD64) location: /truba/home/sariyuka/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 90 [main] DEBUG net.sf.jnati.deploy.NativeLibraryLoader - Loading library: /truba/home/sariyuka/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64/libJniInchi-1.03_1-LINUX-AMD64.so Mapped RXN File /truba/home/sariyuka/reaction-decoder/tests/_ECBLAST_smiles_AAM.rxn Annotated RXN Image /truba/home/sariyuka/reaction-decoder/tests/_ECBLAST_smiles_AAM.png Output is presented in text format: /truba/home/sariyuka/reaction-decoder/tests/_ECBLAST_smiles_AAM.txt